data_2G5R # _entry.id 2G5R # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2G5R pdb_00002g5r 10.2210/pdb2g5r/pdb RCSB RCSB036722 ? ? WWPDB D_1000036722 ? ? # _pdbx_database_status.entry_id 2G5R _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2006-02-23 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Attrill, H.' 1 'Crocker, P.R.' 2 'van Aalten, D.M.' 3 # _citation.id primary _citation.title 'The structure of siglec-7 in complex with sialosides: leads for rational structure-based inhibitor design.' _citation.journal_abbrev Biochem.J. _citation.journal_volume 397 _citation.page_first 271 _citation.page_last 278 _citation.year 2006 _citation.journal_id_ASTM BIJOAK _citation.country UK _citation.journal_id_ISSN 0264-6021 _citation.journal_id_CSD 0043 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16623661 _citation.pdbx_database_id_DOI 10.1042/BJ20060103 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Attrill, H.' 1 ? primary 'Takazawa, H.' 2 ? primary 'Witt, S.' 3 ? primary 'Kelm, S.' 4 ? primary 'Isecke, R.' 5 ? primary 'Brossmer, R.' 6 ? primary 'Ando, T.' 7 ? primary 'Ishida, H.' 8 ? primary 'Kiso, M.' 9 ? primary 'Crocker, P.R.' 10 ? primary 'van Aalten, D.M.' 11 ? # _cell.length_a 52.928 _cell.length_b 52.928 _cell.length_c 93.236 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.entry_id 2G5R _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.entry_id 2G5R _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 92 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Sialic acid-binding Ig-like lectin 7' 14655.292 1 ? ? 'N-terminal domain' ? 2 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 1 ? ? ? ? 3 non-polymer man 'methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' 393.347 1 ? ? ? ? 4 non-polymer syn CYSTEINE 121.158 1 ? ? ? ? 5 water nat water 18.015 102 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Siglec-7, QA79 membrane protein, Adhesion inhibitory receptor molecule 1, AIRM-1, p75, D-siglec, CDw328 antigen' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GQKSNRKDYSLTMQSSVTVQEGMCVHVRCSFSYPVDSQTDSDPVHGYWFRAGNDISWKAPVATNNPAWAVQEETRDRFHL LGDPQTKNCTLSIRDARMSDAGRYFFRMEKGNIKWNYKYDQLSVNVT ; _entity_poly.pdbx_seq_one_letter_code_can ;GQKSNRKDYSLTMQSSVTVQEGMCVHVRCSFSYPVDSQTDSDPVHGYWFRAGNDISWKAPVATNNPAWAVQEETRDRFHL LGDPQTKNCTLSIRDARMSDAGRYFFRMEKGNIKWNYKYDQLSVNVT ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 GLN n 1 3 LYS n 1 4 SER n 1 5 ASN n 1 6 ARG n 1 7 LYS n 1 8 ASP n 1 9 TYR n 1 10 SER n 1 11 LEU n 1 12 THR n 1 13 MET n 1 14 GLN n 1 15 SER n 1 16 SER n 1 17 VAL n 1 18 THR n 1 19 VAL n 1 20 GLN n 1 21 GLU n 1 22 GLY n 1 23 MET n 1 24 CYS n 1 25 VAL n 1 26 HIS n 1 27 VAL n 1 28 ARG n 1 29 CYS n 1 30 SER n 1 31 PHE n 1 32 SER n 1 33 TYR n 1 34 PRO n 1 35 VAL n 1 36 ASP n 1 37 SER n 1 38 GLN n 1 39 THR n 1 40 ASP n 1 41 SER n 1 42 ASP n 1 43 PRO n 1 44 VAL n 1 45 HIS n 1 46 GLY n 1 47 TYR n 1 48 TRP n 1 49 PHE n 1 50 ARG n 1 51 ALA n 1 52 GLY n 1 53 ASN n 1 54 ASP n 1 55 ILE n 1 56 SER n 1 57 TRP n 1 58 LYS n 1 59 ALA n 1 60 PRO n 1 61 VAL n 1 62 ALA n 1 63 THR n 1 64 ASN n 1 65 ASN n 1 66 PRO n 1 67 ALA n 1 68 TRP n 1 69 ALA n 1 70 VAL n 1 71 GLN n 1 72 GLU n 1 73 GLU n 1 74 THR n 1 75 ARG n 1 76 ASP n 1 77 ARG n 1 78 PHE n 1 79 HIS n 1 80 LEU n 1 81 LEU n 1 82 GLY n 1 83 ASP n 1 84 PRO n 1 85 GLN n 1 86 THR n 1 87 LYS n 1 88 ASN n 1 89 CYS n 1 90 THR n 1 91 LEU n 1 92 SER n 1 93 ILE n 1 94 ARG n 1 95 ASP n 1 96 ALA n 1 97 ARG n 1 98 MET n 1 99 SER n 1 100 ASP n 1 101 ALA n 1 102 GLY n 1 103 ARG n 1 104 TYR n 1 105 PHE n 1 106 PHE n 1 107 ARG n 1 108 MET n 1 109 GLU n 1 110 LYS n 1 111 GLY n 1 112 ASN n 1 113 ILE n 1 114 LYS n 1 115 TRP n 1 116 ASN n 1 117 TYR n 1 118 LYS n 1 119 TYR n 1 120 ASP n 1 121 GLN n 1 122 LEU n 1 123 SER n 1 124 VAL n 1 125 ASN n 1 126 VAL n 1 127 THR n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name 'Chinese hamster' _entity_src_gen.pdbx_host_org_scientific_name 'Cricetulus griseus' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 10029 _entity_src_gen.host_org_genus Cricetulus _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell 'CHO Lec1' _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pDEF _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SIGL7_HUMAN _struct_ref.pdbx_db_accession Q9Y286 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;GQKSNRKDYSLTMQSSVTVQEGMCVHVRCSFSYPVDSQTDSDPVHGYWFRAGNDISWKAPVATNNPAWAVQEETRDRFHL LGDPQTKNCTLSIRDARMSDAGRYFFRMEKGNIKWNYKYDQLSVNVT ; _struct_ref.pdbx_align_begin 18 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2G5R _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 127 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9Y286 _struct_ref_seq.db_align_beg 18 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 144 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 18 _struct_ref_seq.pdbx_auth_seq_align_end 144 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE ; 'C8 H15 N O6' 221.208 NXD D-saccharide . 'methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' ;METHYL 5-(ACETYLAMINO)-9-{[AMINO(OXO)ACETYL]AMINO}-3,5,9-TRIDEOXY-D-GLYCERO-ALPHA-D-GLUCO-NON-2-ULOPYRANOSIDONIC ACID; ALPHA METHYL -9-(AMINOOXALYL-AMINO)-9-DEOXYNEU5AC; OXAMIDO-NEU5AC; methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid; methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid; methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-galacto-non-2-ulosidonic acid ; 'C14 H23 N3 O10' 393.347 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2G5R _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.21 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 44.31 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '30% PEG 4000, 0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2003-02-02 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.933 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID14-4' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.933 _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID14-4 # _reflns.entry_id 2G5R _reflns.observed_criterion_sigma_F 2 _reflns.observed_criterion_sigma_I 2 _reflns.d_resolution_high 1.6 _reflns.d_resolution_low 25 _reflns.number_all ? _reflns.number_obs 17748 _reflns.percent_possible_obs 97.5 _reflns.pdbx_Rmerge_I_obs 0.043 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.2 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.6 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 78.9 _reflns_shell.Rmerge_I_obs 0.338 _reflns_shell.meanI_over_sigI_obs 2 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_redundancy 2.2 _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.ls_d_res_high 1.600 _refine.ls_d_res_low 25.000 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 97.560 _refine.ls_number_reflns_obs 17691 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.ls_R_factor_all 0.214 _refine.ls_R_factor_R_work 0.213 _refine.ls_R_factor_R_free 0.228 _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 893 _refine.B_iso_mean 19.424 _refine.aniso_B[1][1] 0.560 _refine.aniso_B[2][2] 0.560 _refine.aniso_B[3][3] -1.130 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.944 _refine.correlation_coeff_Fo_to_Fc_free 0.945 _refine.pdbx_overall_ESU_R 0.101 _refine.pdbx_overall_ESU_R_Free 0.094 _refine.overall_SU_ML 0.063 _refine.overall_SU_B 1.803 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.entry_id 2G5R _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_obs 0.214 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'Siglec-7, APO, 1o7S' _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 904 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 48 _refine_hist.number_atoms_solvent 102 _refine_hist.number_atoms_total 1054 _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 25.000 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 975 0.015 0.021 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1321 1.347 1.961 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 111 6.027 5.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 142 0.097 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 743 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 394 0.186 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 91 0.147 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 25 0.149 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 14 0.124 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 571 1.770 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 912 2.863 3.200 ? 'X-RAY DIFFRACTION' ? r_scbond_it 404 2.448 4.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 409 3.311 3.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.601 _refine_ls_shell.d_res_low 1.642 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.number_reflns_R_work 933 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.27 _refine_ls_shell.R_factor_R_free 0.234 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 59 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 992 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2G5R _struct.title 'Crystal structure of Siglec-7 in complex with methyl-9-(aminooxalyl-amino)-9-deoxyNeu5Ac (oxamido-Neu5Ac)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2G5R _struct_keywords.pdbx_keywords 'CELL ADHESION' _struct_keywords.text 'Siglec, sialic acid, sialoside, CELL ADHESION' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASP A 83 ? LYS A 87 ? ASP A 100 LYS A 104 5 ? 5 HELX_P HELX_P2 2 ARG A 97 ? ALA A 101 ? ARG A 114 ALA A 118 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf none ? A CYS 24 SG ? ? ? 1_555 D CYS . SG ? ? A CYS 41 A CYS 1001 1_555 ? ? ? ? ? ? ? 2.044 ? ? disulf2 disulf ? ? A CYS 29 SG ? ? ? 1_555 A CYS 89 SG ? ? A CYS 46 A CYS 106 1_555 ? ? ? ? ? ? ? 2.005 ? ? covale1 covale one ? B NAG . C1 ? ? ? 1_555 A ASN 88 ND2 ? ? A NAG 1 A ASN 105 1_555 ? ? ? ? ? ? ? 1.432 ? N-Glycosylation # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 2 ? B ? 5 ? C ? 4 ? D ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel B 1 2 ? parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel C 1 2 ? parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel D 1 2 ? anti-parallel D 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 SER A 10 ? THR A 12 ? SER A 27 THR A 29 A 2 SER A 30 ? SER A 32 ? SER A 47 SER A 49 B 1 SER A 16 ? GLN A 20 ? SER A 33 GLN A 37 B 2 LEU A 122 ? THR A 127 ? LEU A 139 THR A 144 B 3 GLY A 102 ? LYS A 110 ? GLY A 119 LYS A 127 B 4 HIS A 45 ? ARG A 50 ? HIS A 62 ARG A 67 B 5 ALA A 62 ? THR A 63 ? ALA A 79 THR A 80 C 1 SER A 16 ? GLN A 20 ? SER A 33 GLN A 37 C 2 LEU A 122 ? THR A 127 ? LEU A 139 THR A 144 C 3 GLY A 102 ? LYS A 110 ? GLY A 119 LYS A 127 C 4 ILE A 113 ? ASN A 116 ? ILE A 130 ASN A 133 D 1 VAL A 25 ? VAL A 27 ? VAL A 42 VAL A 44 D 2 LEU A 91 ? ILE A 93 ? LEU A 108 ILE A 110 D 3 PHE A 78 ? LEU A 80 ? PHE A 95 LEU A 97 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N SER A 10 ? N SER A 27 O SER A 32 ? O SER A 49 B 1 2 N VAL A 17 ? N VAL A 34 O ASN A 125 ? O ASN A 142 B 2 3 O VAL A 124 ? O VAL A 141 N GLY A 102 ? N GLY A 119 B 3 4 O GLU A 109 ? O GLU A 126 N HIS A 45 ? N HIS A 62 B 4 5 N TRP A 48 ? N TRP A 65 O ALA A 62 ? O ALA A 79 C 1 2 N VAL A 17 ? N VAL A 34 O ASN A 125 ? O ASN A 142 C 2 3 O VAL A 124 ? O VAL A 141 N GLY A 102 ? N GLY A 119 C 3 4 N LYS A 110 ? N LYS A 127 O ILE A 113 ? O ILE A 130 D 1 2 N VAL A 27 ? N VAL A 44 O LEU A 91 ? O LEU A 108 D 2 3 O SER A 92 ? O SER A 109 N HIS A 79 ? N HIS A 96 # _atom_sites.entry_id 2G5R _atom_sites.fract_transf_matrix[1][1] 0.018890 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.018890 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.010720 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 18 ? ? ? A . n A 1 2 GLN 2 19 ? ? ? A . n A 1 3 LYS 3 20 ? ? ? A . n A 1 4 SER 4 21 ? ? ? A . n A 1 5 ASN 5 22 ? ? ? A . n A 1 6 ARG 6 23 ? ? ? A . n A 1 7 LYS 7 24 24 LYS ALA A . n A 1 8 ASP 8 25 25 ASP ASP A . n A 1 9 TYR 9 26 26 TYR TYR A . n A 1 10 SER 10 27 27 SER SER A . n A 1 11 LEU 11 28 28 LEU LEU A . n A 1 12 THR 12 29 29 THR THR A . n A 1 13 MET 13 30 30 MET MET A . n A 1 14 GLN 14 31 31 GLN GLN A . n A 1 15 SER 15 32 32 SER SER A . n A 1 16 SER 16 33 33 SER SER A . n A 1 17 VAL 17 34 34 VAL VAL A . n A 1 18 THR 18 35 35 THR THR A . n A 1 19 VAL 19 36 36 VAL VAL A . n A 1 20 GLN 20 37 37 GLN GLN A . n A 1 21 GLU 21 38 38 GLU GLU A . n A 1 22 GLY 22 39 39 GLY GLY A . n A 1 23 MET 23 40 40 MET MET A . n A 1 24 CYS 24 41 41 CYS CYS A . n A 1 25 VAL 25 42 42 VAL VAL A . n A 1 26 HIS 26 43 43 HIS HIS A . n A 1 27 VAL 27 44 44 VAL VAL A . n A 1 28 ARG 28 45 45 ARG ARG A . n A 1 29 CYS 29 46 46 CYS CYS A . n A 1 30 SER 30 47 47 SER SER A . n A 1 31 PHE 31 48 48 PHE PHE A . n A 1 32 SER 32 49 49 SER SER A . n A 1 33 TYR 33 50 50 TYR TYR A . n A 1 34 PRO 34 51 51 PRO PRO A . n A 1 35 VAL 35 52 ? ? ? A . n A 1 36 ASP 36 53 ? ? ? A . n A 1 37 SER 37 54 54 SER SER A . n A 1 38 GLN 38 55 55 GLN ALA A . n A 1 39 THR 39 56 56 THR THR A . n A 1 40 ASP 40 57 57 ASP ALA A . n A 1 41 SER 41 58 58 SER SER A . n A 1 42 ASP 42 59 59 ASP ALA A . n A 1 43 PRO 43 60 60 PRO PRO A . n A 1 44 VAL 44 61 61 VAL VAL A . n A 1 45 HIS 45 62 62 HIS HIS A . n A 1 46 GLY 46 63 63 GLY GLY A . n A 1 47 TYR 47 64 64 TYR TYR A . n A 1 48 TRP 48 65 65 TRP TRP A . n A 1 49 PHE 49 66 66 PHE PHE A . n A 1 50 ARG 50 67 67 ARG ARG A . n A 1 51 ALA 51 68 68 ALA ALA A . n A 1 52 GLY 52 69 69 GLY GLY A . n A 1 53 ASN 53 70 ? ? ? A . n A 1 54 ASP 54 71 ? ? ? A . n A 1 55 ILE 55 72 ? ? ? A . n A 1 56 SER 56 73 ? ? ? A . n A 1 57 TRP 57 74 ? ? ? A . n A 1 58 LYS 58 75 75 LYS ALA A . n A 1 59 ALA 59 76 76 ALA ALA A . n A 1 60 PRO 60 77 77 PRO PRO A . n A 1 61 VAL 61 78 78 VAL VAL A . n A 1 62 ALA 62 79 79 ALA ALA A . n A 1 63 THR 63 80 80 THR THR A . n A 1 64 ASN 64 81 81 ASN ASN A . n A 1 65 ASN 65 82 82 ASN ASN A . n A 1 66 PRO 66 83 83 PRO PRO A . n A 1 67 ALA 67 84 84 ALA ALA A . n A 1 68 TRP 68 85 85 TRP TRP A . n A 1 69 ALA 69 86 86 ALA ALA A . n A 1 70 VAL 70 87 87 VAL VAL A . n A 1 71 GLN 71 88 88 GLN GLN A . n A 1 72 GLU 72 89 89 GLU GLU A . n A 1 73 GLU 73 90 90 GLU GLU A . n A 1 74 THR 74 91 91 THR THR A . n A 1 75 ARG 75 92 92 ARG ARG A . n A 1 76 ASP 76 93 93 ASP ASP A . n A 1 77 ARG 77 94 94 ARG ARG A . n A 1 78 PHE 78 95 95 PHE PHE A . n A 1 79 HIS 79 96 96 HIS HIS A . n A 1 80 LEU 80 97 97 LEU LEU A . n A 1 81 LEU 81 98 98 LEU LEU A . n A 1 82 GLY 82 99 99 GLY GLY A . n A 1 83 ASP 83 100 100 ASP ASP A . n A 1 84 PRO 84 101 101 PRO PRO A . n A 1 85 GLN 85 102 102 GLN GLN A . n A 1 86 THR 86 103 103 THR THR A . n A 1 87 LYS 87 104 104 LYS LYS A . n A 1 88 ASN 88 105 105 ASN ASN A . n A 1 89 CYS 89 106 106 CYS CYS A . n A 1 90 THR 90 107 107 THR THR A . n A 1 91 LEU 91 108 108 LEU LEU A . n A 1 92 SER 92 109 109 SER SER A . n A 1 93 ILE 93 110 110 ILE ILE A . n A 1 94 ARG 94 111 111 ARG ARG A . n A 1 95 ASP 95 112 112 ASP ASP A . n A 1 96 ALA 96 113 113 ALA ALA A . n A 1 97 ARG 97 114 114 ARG ARG A . n A 1 98 MET 98 115 115 MET MET A . n A 1 99 SER 99 116 116 SER SER A . n A 1 100 ASP 100 117 117 ASP ASP A . n A 1 101 ALA 101 118 118 ALA ALA A . n A 1 102 GLY 102 119 119 GLY GLY A . n A 1 103 ARG 103 120 120 ARG ARG A . n A 1 104 TYR 104 121 121 TYR TYR A . n A 1 105 PHE 105 122 122 PHE PHE A . n A 1 106 PHE 106 123 123 PHE PHE A . n A 1 107 ARG 107 124 124 ARG ARG A . n A 1 108 MET 108 125 125 MET MET A . n A 1 109 GLU 109 126 126 GLU GLU A . n A 1 110 LYS 110 127 127 LYS LYS A . n A 1 111 GLY 111 128 128 GLY GLY A . n A 1 112 ASN 112 129 129 ASN ASN A . n A 1 113 ILE 113 130 130 ILE ILE A . n A 1 114 LYS 114 131 131 LYS LYS A . n A 1 115 TRP 115 132 132 TRP TRP A . n A 1 116 ASN 116 133 133 ASN ASN A . n A 1 117 TYR 117 134 134 TYR TYR A . n A 1 118 LYS 118 135 135 LYS LYS A . n A 1 119 TYR 119 136 136 TYR TYR A . n A 1 120 ASP 120 137 137 ASP ASP A . n A 1 121 GLN 121 138 138 GLN GLN A . n A 1 122 LEU 122 139 139 LEU LEU A . n A 1 123 SER 123 140 140 SER SER A . n A 1 124 VAL 124 141 141 VAL VAL A . n A 1 125 ASN 125 142 142 ASN ASN A . n A 1 126 VAL 126 143 143 VAL VAL A . n A 1 127 THR 127 144 144 THR THR A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NAG 1 1 1 NAG NAG A . C 3 NXD 1 145 1 NXD NXD A . D 4 CYS 1 1001 1 CYS CYS A . E 5 HOH 1 1002 2 HOH HOH A . E 5 HOH 2 1003 3 HOH HOH A . E 5 HOH 3 1004 4 HOH HOH A . E 5 HOH 4 1005 5 HOH HOH A . E 5 HOH 5 1006 6 HOH HOH A . E 5 HOH 6 1007 7 HOH HOH A . E 5 HOH 7 1008 8 HOH HOH A . E 5 HOH 8 1009 9 HOH HOH A . E 5 HOH 9 1010 10 HOH HOH A . E 5 HOH 10 1011 11 HOH HOH A . E 5 HOH 11 1012 12 HOH HOH A . E 5 HOH 12 1013 13 HOH HOH A . E 5 HOH 13 1014 14 HOH HOH A . E 5 HOH 14 1015 15 HOH HOH A . E 5 HOH 15 1016 16 HOH HOH A . E 5 HOH 16 1017 17 HOH HOH A . E 5 HOH 17 1018 18 HOH HOH A . E 5 HOH 18 1019 19 HOH HOH A . E 5 HOH 19 1020 20 HOH HOH A . E 5 HOH 20 1021 21 HOH HOH A . E 5 HOH 21 1022 22 HOH HOH A . E 5 HOH 22 1023 23 HOH HOH A . E 5 HOH 23 1024 24 HOH HOH A . E 5 HOH 24 1025 25 HOH HOH A . E 5 HOH 25 1026 26 HOH HOH A . E 5 HOH 26 1027 27 HOH HOH A . E 5 HOH 27 1028 28 HOH HOH A . E 5 HOH 28 1029 29 HOH HOH A . E 5 HOH 29 1030 30 HOH HOH A . E 5 HOH 30 1031 32 HOH HOH A . E 5 HOH 31 1032 33 HOH HOH A . E 5 HOH 32 1033 34 HOH HOH A . E 5 HOH 33 1034 35 HOH HOH A . E 5 HOH 34 1035 36 HOH HOH A . E 5 HOH 35 1036 37 HOH HOH A . E 5 HOH 36 1037 38 HOH HOH A . E 5 HOH 37 1038 39 HOH HOH A . E 5 HOH 38 1039 40 HOH HOH A . E 5 HOH 39 1040 41 HOH HOH A . E 5 HOH 40 1041 42 HOH HOH A . E 5 HOH 41 1042 43 HOH HOH A . E 5 HOH 42 1043 44 HOH HOH A . E 5 HOH 43 1044 45 HOH HOH A . E 5 HOH 44 1045 46 HOH HOH A . E 5 HOH 45 1046 47 HOH HOH A . E 5 HOH 46 1047 48 HOH HOH A . E 5 HOH 47 1048 49 HOH HOH A . E 5 HOH 48 1049 50 HOH HOH A . E 5 HOH 49 1050 51 HOH HOH A . E 5 HOH 50 1051 52 HOH HOH A . E 5 HOH 51 1052 53 HOH HOH A . E 5 HOH 52 1053 54 HOH HOH A . E 5 HOH 53 1054 55 HOH HOH A . E 5 HOH 54 1055 56 HOH HOH A . E 5 HOH 55 1056 57 HOH HOH A . E 5 HOH 56 1057 58 HOH HOH A . E 5 HOH 57 1058 59 HOH HOH A . E 5 HOH 58 1059 60 HOH HOH A . E 5 HOH 59 1060 62 HOH HOH A . E 5 HOH 60 1061 63 HOH HOH A . E 5 HOH 61 1062 64 HOH HOH A . E 5 HOH 62 1063 65 HOH HOH A . E 5 HOH 63 1064 66 HOH HOH A . E 5 HOH 64 1065 67 HOH HOH A . E 5 HOH 65 1066 68 HOH HOH A . E 5 HOH 66 1067 69 HOH HOH A . E 5 HOH 67 1068 70 HOH HOH A . E 5 HOH 68 1069 71 HOH HOH A . E 5 HOH 69 1070 72 HOH HOH A . E 5 HOH 70 1071 73 HOH HOH A . E 5 HOH 71 1072 74 HOH HOH A . E 5 HOH 72 1073 75 HOH HOH A . E 5 HOH 73 1074 76 HOH HOH A . E 5 HOH 74 1075 77 HOH HOH A . E 5 HOH 75 1076 78 HOH HOH A . E 5 HOH 76 1077 79 HOH HOH A . E 5 HOH 77 1078 80 HOH HOH A . E 5 HOH 78 1079 81 HOH HOH A . E 5 HOH 79 1080 82 HOH HOH A . E 5 HOH 80 1081 83 HOH HOH A . E 5 HOH 81 1082 84 HOH HOH A . E 5 HOH 82 1083 85 HOH HOH A . E 5 HOH 83 1084 91 HOH HOH A . E 5 HOH 84 1085 95 HOH HOH A . E 5 HOH 85 1086 99 HOH HOH A . E 5 HOH 86 1087 110 HOH HOH A . E 5 HOH 87 1088 111 HOH HOH A . E 5 HOH 88 1089 112 HOH HOH A . E 5 HOH 89 1090 114 HOH HOH A . E 5 HOH 90 1091 115 HOH HOH A . E 5 HOH 91 1092 117 HOH HOH A . E 5 HOH 92 1093 118 HOH HOH A . E 5 HOH 93 1094 121 HOH HOH A . E 5 HOH 94 1095 124 HOH HOH A . E 5 HOH 95 1096 125 HOH HOH A . E 5 HOH 96 1097 127 HOH HOH A . E 5 HOH 97 1098 128 HOH HOH A . E 5 HOH 98 1099 130 HOH HOH A . E 5 HOH 99 1100 134 HOH HOH A . E 5 HOH 100 1101 136 HOH HOH A . E 5 HOH 101 1102 144 HOH HOH A . E 5 HOH 102 1103 146 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id ASN _pdbx_struct_mod_residue.label_seq_id 88 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id ASN _pdbx_struct_mod_residue.auth_seq_id 105 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id ASN _pdbx_struct_mod_residue.details 'GLYCOSYLATION SITE' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-06-20 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2020-07-29 5 'Structure model' 2 1 2023-10-25 6 'Structure model' 2 2 2023-11-15 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Atomic model' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' 'Data collection' 9 5 'Structure model' 'Database references' 10 5 'Structure model' 'Refinement description' 11 5 'Structure model' 'Structure summary' 12 6 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' atom_site 2 4 'Structure model' chem_comp 3 4 'Structure model' entity 4 4 'Structure model' pdbx_chem_comp_identifier 5 4 'Structure model' pdbx_entity_nonpoly 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site 8 4 'Structure model' struct_site_gen 9 5 'Structure model' chem_comp 10 5 'Structure model' chem_comp_atom 11 5 'Structure model' chem_comp_bond 12 5 'Structure model' database_2 13 5 'Structure model' pdbx_initial_refinement_model 14 6 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_atom_site.auth_atom_id' 2 4 'Structure model' '_atom_site.label_atom_id' 3 4 'Structure model' '_chem_comp.name' 4 4 'Structure model' '_chem_comp.pdbx_synonyms' 5 4 'Structure model' '_chem_comp.type' 6 4 'Structure model' '_entity.pdbx_description' 7 4 'Structure model' '_pdbx_entity_nonpoly.name' 8 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 9 4 'Structure model' '_struct_conn.pdbx_role' 10 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 11 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 13 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 14 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 15 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 16 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 17 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 19 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 20 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 21 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 22 5 'Structure model' '_chem_comp.pdbx_synonyms' 23 5 'Structure model' '_database_2.pdbx_DOI' 24 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 10.7764 _pdbx_refine_tls.origin_y 10.1270 _pdbx_refine_tls.origin_z 19.8213 _pdbx_refine_tls.T[1][1] 0.1391 _pdbx_refine_tls.T[2][2] 0.0042 _pdbx_refine_tls.T[3][3] 0.0648 _pdbx_refine_tls.T[1][2] 0.0239 _pdbx_refine_tls.T[1][3] 0.0478 _pdbx_refine_tls.T[2][3] 0.0098 _pdbx_refine_tls.L[1][1] 0.6945 _pdbx_refine_tls.L[2][2] 1.7583 _pdbx_refine_tls.L[3][3] 3.1111 _pdbx_refine_tls.L[1][2] 0.1996 _pdbx_refine_tls.L[1][3] -0.3042 _pdbx_refine_tls.L[2][3] -1.6745 _pdbx_refine_tls.S[1][1] 0.0604 _pdbx_refine_tls.S[2][2] 0.0953 _pdbx_refine_tls.S[3][3] -0.1556 _pdbx_refine_tls.S[1][2] 0.0186 _pdbx_refine_tls.S[1][3] -0.0241 _pdbx_refine_tls.S[2][3] 0.1108 _pdbx_refine_tls.S[2][1] 0.3748 _pdbx_refine_tls.S[3][1] -0.4243 _pdbx_refine_tls.S[3][2] -0.0939 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 7 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 127 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 24 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 144 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.1.24 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran ? 1 PDB_EXTRACT 1.701 'Nov. 1, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 2 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 3 SCALEPACK . ? ? ? ? 'data scaling' ? ? ? 4 AMoRE . ? ? ? ? phasing ? ? ? 5 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 CB A SER 27 ? ? OG A SER 27 ? ? 1.519 1.418 0.101 0.013 N 2 1 C A SER 49 ? ? N A TYR 50 ? ? 1.509 1.336 0.173 0.023 Y 3 1 C A PRO 51 ? ? O A PRO 51 ? ? 1.420 1.228 0.192 0.020 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 TYR A 50 ? ? -171.25 149.35 2 1 THR A 56 ? ? -83.79 34.61 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 24 ? N ? A LYS 7 N 2 1 Y 1 A LYS 24 ? CG ? A LYS 7 CG 3 1 Y 1 A LYS 24 ? CD ? A LYS 7 CD 4 1 Y 1 A LYS 24 ? CE ? A LYS 7 CE 5 1 Y 1 A LYS 24 ? NZ ? A LYS 7 NZ 6 1 Y 1 A GLN 55 ? CG ? A GLN 38 CG 7 1 Y 1 A GLN 55 ? CD ? A GLN 38 CD 8 1 Y 1 A GLN 55 ? OE1 ? A GLN 38 OE1 9 1 Y 1 A GLN 55 ? NE2 ? A GLN 38 NE2 10 1 Y 1 A ASP 57 ? CG ? A ASP 40 CG 11 1 Y 1 A ASP 57 ? OD1 ? A ASP 40 OD1 12 1 Y 1 A ASP 57 ? OD2 ? A ASP 40 OD2 13 1 Y 1 A ASP 59 ? CG ? A ASP 42 CG 14 1 Y 1 A ASP 59 ? OD1 ? A ASP 42 OD1 15 1 Y 1 A ASP 59 ? OD2 ? A ASP 42 OD2 16 1 Y 1 A LYS 75 ? CG ? A LYS 58 CG 17 1 Y 1 A LYS 75 ? CD ? A LYS 58 CD 18 1 Y 1 A LYS 75 ? CE ? A LYS 58 CE 19 1 Y 1 A LYS 75 ? NZ ? A LYS 58 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 18 ? A GLY 1 2 1 Y 1 A GLN 19 ? A GLN 2 3 1 Y 1 A LYS 20 ? A LYS 3 4 1 Y 1 A SER 21 ? A SER 4 5 1 Y 1 A ASN 22 ? A ASN 5 6 1 Y 1 A ARG 23 ? A ARG 6 7 1 Y 1 A VAL 52 ? A VAL 35 8 1 Y 1 A ASP 53 ? A ASP 36 9 1 Y 1 A ASN 70 ? A ASN 53 10 1 Y 1 A ASP 71 ? A ASP 54 11 1 Y 1 A ILE 72 ? A ILE 55 12 1 Y 1 A SER 73 ? A SER 56 13 1 Y 1 A TRP 74 ? A TRP 57 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 GLN N N N N 88 GLN CA C N S 89 GLN C C N N 90 GLN O O N N 91 GLN CB C N N 92 GLN CG C N N 93 GLN CD C N N 94 GLN OE1 O N N 95 GLN NE2 N N N 96 GLN OXT O N N 97 GLN H H N N 98 GLN H2 H N N 99 GLN HA H N N 100 GLN HB2 H N N 101 GLN HB3 H N N 102 GLN HG2 H N N 103 GLN HG3 H N N 104 GLN HE21 H N N 105 GLN HE22 H N N 106 GLN HXT H N N 107 GLU N N N N 108 GLU CA C N S 109 GLU C C N N 110 GLU O O N N 111 GLU CB C N N 112 GLU CG C N N 113 GLU CD C N N 114 GLU OE1 O N N 115 GLU OE2 O N N 116 GLU OXT O N N 117 GLU H H N N 118 GLU H2 H N N 119 GLU HA H N N 120 GLU HB2 H N N 121 GLU HB3 H N N 122 GLU HG2 H N N 123 GLU HG3 H N N 124 GLU HE2 H N N 125 GLU HXT H N N 126 GLY N N N N 127 GLY CA C N N 128 GLY C C N N 129 GLY O O N N 130 GLY OXT O N N 131 GLY H H N N 132 GLY H2 H N N 133 GLY HA2 H N N 134 GLY HA3 H N N 135 GLY HXT H N N 136 HIS N N N N 137 HIS CA C N S 138 HIS C C N N 139 HIS O O N N 140 HIS CB C N N 141 HIS CG C Y N 142 HIS ND1 N Y N 143 HIS CD2 C Y N 144 HIS CE1 C Y N 145 HIS NE2 N Y N 146 HIS OXT O N N 147 HIS H H N N 148 HIS H2 H N N 149 HIS HA H N N 150 HIS HB2 H N N 151 HIS HB3 H N N 152 HIS HD1 H N N 153 HIS HD2 H N N 154 HIS HE1 H N N 155 HIS HE2 H N N 156 HIS HXT H N N 157 HOH O O N N 158 HOH H1 H N N 159 HOH H2 H N N 160 ILE N N N N 161 ILE CA C N S 162 ILE C C N N 163 ILE O O N N 164 ILE CB C N S 165 ILE CG1 C N N 166 ILE CG2 C N N 167 ILE CD1 C N N 168 ILE OXT O N N 169 ILE H H N N 170 ILE H2 H N N 171 ILE HA H N N 172 ILE HB H N N 173 ILE HG12 H N N 174 ILE HG13 H N N 175 ILE HG21 H N N 176 ILE HG22 H N N 177 ILE HG23 H N N 178 ILE HD11 H N N 179 ILE HD12 H N N 180 ILE HD13 H N N 181 ILE HXT H N N 182 LEU N N N N 183 LEU CA C N S 184 LEU C C N N 185 LEU O O N N 186 LEU CB C N N 187 LEU CG C N N 188 LEU CD1 C N N 189 LEU CD2 C N N 190 LEU OXT O N N 191 LEU H H N N 192 LEU H2 H N N 193 LEU HA H N N 194 LEU HB2 H N N 195 LEU HB3 H N N 196 LEU HG H N N 197 LEU HD11 H N N 198 LEU HD12 H N N 199 LEU HD13 H N N 200 LEU HD21 H N N 201 LEU HD22 H N N 202 LEU HD23 H N N 203 LEU HXT H N N 204 LYS N N N N 205 LYS CA C N S 206 LYS C C N N 207 LYS O O N N 208 LYS CB C N N 209 LYS CG C N N 210 LYS CD C N N 211 LYS CE C N N 212 LYS NZ N N N 213 LYS OXT O N N 214 LYS H H N N 215 LYS H2 H N N 216 LYS HA H N N 217 LYS HB2 H N N 218 LYS HB3 H N N 219 LYS HG2 H N N 220 LYS HG3 H N N 221 LYS HD2 H N N 222 LYS HD3 H N N 223 LYS HE2 H N N 224 LYS HE3 H N N 225 LYS HZ1 H N N 226 LYS HZ2 H N N 227 LYS HZ3 H N N 228 LYS HXT H N N 229 MET N N N N 230 MET CA C N S 231 MET C C N N 232 MET O O N N 233 MET CB C N N 234 MET CG C N N 235 MET SD S N N 236 MET CE C N N 237 MET OXT O N N 238 MET H H N N 239 MET H2 H N N 240 MET HA H N N 241 MET HB2 H N N 242 MET HB3 H N N 243 MET HG2 H N N 244 MET HG3 H N N 245 MET HE1 H N N 246 MET HE2 H N N 247 MET HE3 H N N 248 MET HXT H N N 249 NAG C1 C N R 250 NAG C2 C N R 251 NAG C3 C N R 252 NAG C4 C N S 253 NAG C5 C N R 254 NAG C6 C N N 255 NAG C7 C N N 256 NAG C8 C N N 257 NAG N2 N N N 258 NAG O1 O N N 259 NAG O3 O N N 260 NAG O4 O N N 261 NAG O5 O N N 262 NAG O6 O N N 263 NAG O7 O N N 264 NAG H1 H N N 265 NAG H2 H N N 266 NAG H3 H N N 267 NAG H4 H N N 268 NAG H5 H N N 269 NAG H61 H N N 270 NAG H62 H N N 271 NAG H81 H N N 272 NAG H82 H N N 273 NAG H83 H N N 274 NAG HN2 H N N 275 NAG HO1 H N N 276 NAG HO3 H N N 277 NAG HO4 H N N 278 NAG HO6 H N N 279 NXD C11 C N N 280 NXD C10 C N N 281 NXD O10 O N N 282 NXD N5 N N N 283 NXD C5 C N R 284 NXD C4 C N S 285 NXD O4 O N N 286 NXD C3 C N N 287 NXD C2 C N R 288 NXD C1 C N N 289 NXD O1B O N N 290 NXD O1A O N N 291 NXD O2 O N N 292 NXD CB C N N 293 NXD O6 O N N 294 NXD C6 C N R 295 NXD C7 C N R 296 NXD O7 O N N 297 NXD C8 C N R 298 NXD O8 O N N 299 NXD C9 C N N 300 NXD NAB N N N 301 NXD CAC C N N 302 NXD OAD O N N 303 NXD CAF C N N 304 NXD OAG O N N 305 NXD NAK N N N 306 NXD H111 H N N 307 NXD H113 H N N 308 NXD H112 H N N 309 NXD HN5 H N N 310 NXD H5 H N N 311 NXD H4 H N N 312 NXD HO4 H N N 313 NXD H32 H N N 314 NXD H31 H N N 315 NXD HO1B H N N 316 NXD HB1 H N N 317 NXD HB2 H N N 318 NXD HB3 H N N 319 NXD H6 H N N 320 NXD H7 H N N 321 NXD HO7 H N N 322 NXD H8 H N N 323 NXD HO8 H N N 324 NXD H92 H N N 325 NXD H91 H N N 326 NXD HAB H N N 327 NXD HAK1 H N N 328 NXD HAK2 H N N 329 PHE N N N N 330 PHE CA C N S 331 PHE C C N N 332 PHE O O N N 333 PHE CB C N N 334 PHE CG C Y N 335 PHE CD1 C Y N 336 PHE CD2 C Y N 337 PHE CE1 C Y N 338 PHE CE2 C Y N 339 PHE CZ C Y N 340 PHE OXT O N N 341 PHE H H N N 342 PHE H2 H N N 343 PHE HA H N N 344 PHE HB2 H N N 345 PHE HB3 H N N 346 PHE HD1 H N N 347 PHE HD2 H N N 348 PHE HE1 H N N 349 PHE HE2 H N N 350 PHE HZ H N N 351 PHE HXT H N N 352 PRO N N N N 353 PRO CA C N S 354 PRO C C N N 355 PRO O O N N 356 PRO CB C N N 357 PRO CG C N N 358 PRO CD C N N 359 PRO OXT O N N 360 PRO H H N N 361 PRO HA H N N 362 PRO HB2 H N N 363 PRO HB3 H N N 364 PRO HG2 H N N 365 PRO HG3 H N N 366 PRO HD2 H N N 367 PRO HD3 H N N 368 PRO HXT H N N 369 SER N N N N 370 SER CA C N S 371 SER C C N N 372 SER O O N N 373 SER CB C N N 374 SER OG O N N 375 SER OXT O N N 376 SER H H N N 377 SER H2 H N N 378 SER HA H N N 379 SER HB2 H N N 380 SER HB3 H N N 381 SER HG H N N 382 SER HXT H N N 383 THR N N N N 384 THR CA C N S 385 THR C C N N 386 THR O O N N 387 THR CB C N R 388 THR OG1 O N N 389 THR CG2 C N N 390 THR OXT O N N 391 THR H H N N 392 THR H2 H N N 393 THR HA H N N 394 THR HB H N N 395 THR HG1 H N N 396 THR HG21 H N N 397 THR HG22 H N N 398 THR HG23 H N N 399 THR HXT H N N 400 TRP N N N N 401 TRP CA C N S 402 TRP C C N N 403 TRP O O N N 404 TRP CB C N N 405 TRP CG C Y N 406 TRP CD1 C Y N 407 TRP CD2 C Y N 408 TRP NE1 N Y N 409 TRP CE2 C Y N 410 TRP CE3 C Y N 411 TRP CZ2 C Y N 412 TRP CZ3 C Y N 413 TRP CH2 C Y N 414 TRP OXT O N N 415 TRP H H N N 416 TRP H2 H N N 417 TRP HA H N N 418 TRP HB2 H N N 419 TRP HB3 H N N 420 TRP HD1 H N N 421 TRP HE1 H N N 422 TRP HE3 H N N 423 TRP HZ2 H N N 424 TRP HZ3 H N N 425 TRP HH2 H N N 426 TRP HXT H N N 427 TYR N N N N 428 TYR CA C N S 429 TYR C C N N 430 TYR O O N N 431 TYR CB C N N 432 TYR CG C Y N 433 TYR CD1 C Y N 434 TYR CD2 C Y N 435 TYR CE1 C Y N 436 TYR CE2 C Y N 437 TYR CZ C Y N 438 TYR OH O N N 439 TYR OXT O N N 440 TYR H H N N 441 TYR H2 H N N 442 TYR HA H N N 443 TYR HB2 H N N 444 TYR HB3 H N N 445 TYR HD1 H N N 446 TYR HD2 H N N 447 TYR HE1 H N N 448 TYR HE2 H N N 449 TYR HH H N N 450 TYR HXT H N N 451 VAL N N N N 452 VAL CA C N S 453 VAL C C N N 454 VAL O O N N 455 VAL CB C N N 456 VAL CG1 C N N 457 VAL CG2 C N N 458 VAL OXT O N N 459 VAL H H N N 460 VAL H2 H N N 461 VAL HA H N N 462 VAL HB H N N 463 VAL HG11 H N N 464 VAL HG12 H N N 465 VAL HG13 H N N 466 VAL HG21 H N N 467 VAL HG22 H N N 468 VAL HG23 H N N 469 VAL HXT H N N 470 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 GLN N CA sing N N 83 GLN N H sing N N 84 GLN N H2 sing N N 85 GLN CA C sing N N 86 GLN CA CB sing N N 87 GLN CA HA sing N N 88 GLN C O doub N N 89 GLN C OXT sing N N 90 GLN CB CG sing N N 91 GLN CB HB2 sing N N 92 GLN CB HB3 sing N N 93 GLN CG CD sing N N 94 GLN CG HG2 sing N N 95 GLN CG HG3 sing N N 96 GLN CD OE1 doub N N 97 GLN CD NE2 sing N N 98 GLN NE2 HE21 sing N N 99 GLN NE2 HE22 sing N N 100 GLN OXT HXT sing N N 101 GLU N CA sing N N 102 GLU N H sing N N 103 GLU N H2 sing N N 104 GLU CA C sing N N 105 GLU CA CB sing N N 106 GLU CA HA sing N N 107 GLU C O doub N N 108 GLU C OXT sing N N 109 GLU CB CG sing N N 110 GLU CB HB2 sing N N 111 GLU CB HB3 sing N N 112 GLU CG CD sing N N 113 GLU CG HG2 sing N N 114 GLU CG HG3 sing N N 115 GLU CD OE1 doub N N 116 GLU CD OE2 sing N N 117 GLU OE2 HE2 sing N N 118 GLU OXT HXT sing N N 119 GLY N CA sing N N 120 GLY N H sing N N 121 GLY N H2 sing N N 122 GLY CA C sing N N 123 GLY CA HA2 sing N N 124 GLY CA HA3 sing N N 125 GLY C O doub N N 126 GLY C OXT sing N N 127 GLY OXT HXT sing N N 128 HIS N CA sing N N 129 HIS N H sing N N 130 HIS N H2 sing N N 131 HIS CA C sing N N 132 HIS CA CB sing N N 133 HIS CA HA sing N N 134 HIS C O doub N N 135 HIS C OXT sing N N 136 HIS CB CG sing N N 137 HIS CB HB2 sing N N 138 HIS CB HB3 sing N N 139 HIS CG ND1 sing Y N 140 HIS CG CD2 doub Y N 141 HIS ND1 CE1 doub Y N 142 HIS ND1 HD1 sing N N 143 HIS CD2 NE2 sing Y N 144 HIS CD2 HD2 sing N N 145 HIS CE1 NE2 sing Y N 146 HIS CE1 HE1 sing N N 147 HIS NE2 HE2 sing N N 148 HIS OXT HXT sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 ILE N CA sing N N 152 ILE N H sing N N 153 ILE N H2 sing N N 154 ILE CA C sing N N 155 ILE CA CB sing N N 156 ILE CA HA sing N N 157 ILE C O doub N N 158 ILE C OXT sing N N 159 ILE CB CG1 sing N N 160 ILE CB CG2 sing N N 161 ILE CB HB sing N N 162 ILE CG1 CD1 sing N N 163 ILE CG1 HG12 sing N N 164 ILE CG1 HG13 sing N N 165 ILE CG2 HG21 sing N N 166 ILE CG2 HG22 sing N N 167 ILE CG2 HG23 sing N N 168 ILE CD1 HD11 sing N N 169 ILE CD1 HD12 sing N N 170 ILE CD1 HD13 sing N N 171 ILE OXT HXT sing N N 172 LEU N CA sing N N 173 LEU N H sing N N 174 LEU N H2 sing N N 175 LEU CA C sing N N 176 LEU CA CB sing N N 177 LEU CA HA sing N N 178 LEU C O doub N N 179 LEU C OXT sing N N 180 LEU CB CG sing N N 181 LEU CB HB2 sing N N 182 LEU CB HB3 sing N N 183 LEU CG CD1 sing N N 184 LEU CG CD2 sing N N 185 LEU CG HG sing N N 186 LEU CD1 HD11 sing N N 187 LEU CD1 HD12 sing N N 188 LEU CD1 HD13 sing N N 189 LEU CD2 HD21 sing N N 190 LEU CD2 HD22 sing N N 191 LEU CD2 HD23 sing N N 192 LEU OXT HXT sing N N 193 LYS N CA sing N N 194 LYS N H sing N N 195 LYS N H2 sing N N 196 LYS CA C sing N N 197 LYS CA CB sing N N 198 LYS CA HA sing N N 199 LYS C O doub N N 200 LYS C OXT sing N N 201 LYS CB CG sing N N 202 LYS CB HB2 sing N N 203 LYS CB HB3 sing N N 204 LYS CG CD sing N N 205 LYS CG HG2 sing N N 206 LYS CG HG3 sing N N 207 LYS CD CE sing N N 208 LYS CD HD2 sing N N 209 LYS CD HD3 sing N N 210 LYS CE NZ sing N N 211 LYS CE HE2 sing N N 212 LYS CE HE3 sing N N 213 LYS NZ HZ1 sing N N 214 LYS NZ HZ2 sing N N 215 LYS NZ HZ3 sing N N 216 LYS OXT HXT sing N N 217 MET N CA sing N N 218 MET N H sing N N 219 MET N H2 sing N N 220 MET CA C sing N N 221 MET CA CB sing N N 222 MET CA HA sing N N 223 MET C O doub N N 224 MET C OXT sing N N 225 MET CB CG sing N N 226 MET CB HB2 sing N N 227 MET CB HB3 sing N N 228 MET CG SD sing N N 229 MET CG HG2 sing N N 230 MET CG HG3 sing N N 231 MET SD CE sing N N 232 MET CE HE1 sing N N 233 MET CE HE2 sing N N 234 MET CE HE3 sing N N 235 MET OXT HXT sing N N 236 NAG C1 C2 sing N N 237 NAG C1 O1 sing N N 238 NAG C1 O5 sing N N 239 NAG C1 H1 sing N N 240 NAG C2 C3 sing N N 241 NAG C2 N2 sing N N 242 NAG C2 H2 sing N N 243 NAG C3 C4 sing N N 244 NAG C3 O3 sing N N 245 NAG C3 H3 sing N N 246 NAG C4 C5 sing N N 247 NAG C4 O4 sing N N 248 NAG C4 H4 sing N N 249 NAG C5 C6 sing N N 250 NAG C5 O5 sing N N 251 NAG C5 H5 sing N N 252 NAG C6 O6 sing N N 253 NAG C6 H61 sing N N 254 NAG C6 H62 sing N N 255 NAG C7 C8 sing N N 256 NAG C7 N2 sing N N 257 NAG C7 O7 doub N N 258 NAG C8 H81 sing N N 259 NAG C8 H82 sing N N 260 NAG C8 H83 sing N N 261 NAG N2 HN2 sing N N 262 NAG O1 HO1 sing N N 263 NAG O3 HO3 sing N N 264 NAG O4 HO4 sing N N 265 NAG O6 HO6 sing N N 266 NXD C11 C10 sing N N 267 NXD C11 H111 sing N N 268 NXD C11 H113 sing N N 269 NXD C11 H112 sing N N 270 NXD C10 O10 doub N N 271 NXD C10 N5 sing N N 272 NXD N5 C5 sing N N 273 NXD N5 HN5 sing N N 274 NXD C5 C4 sing N N 275 NXD C5 C6 sing N N 276 NXD C5 H5 sing N N 277 NXD C4 O4 sing N N 278 NXD C4 C3 sing N N 279 NXD C4 H4 sing N N 280 NXD O4 HO4 sing N N 281 NXD C3 C2 sing N N 282 NXD C3 H32 sing N N 283 NXD C3 H31 sing N N 284 NXD C2 C1 sing N N 285 NXD C2 O2 sing N N 286 NXD C2 O6 sing N N 287 NXD C1 O1B sing N N 288 NXD C1 O1A doub N N 289 NXD O1B HO1B sing N N 290 NXD O2 CB sing N N 291 NXD CB HB1 sing N N 292 NXD CB HB2 sing N N 293 NXD CB HB3 sing N N 294 NXD O6 C6 sing N N 295 NXD C6 C7 sing N N 296 NXD C6 H6 sing N N 297 NXD C7 O7 sing N N 298 NXD C7 C8 sing N N 299 NXD C7 H7 sing N N 300 NXD O7 HO7 sing N N 301 NXD C8 O8 sing N N 302 NXD C8 C9 sing N N 303 NXD C8 H8 sing N N 304 NXD O8 HO8 sing N N 305 NXD C9 NAB sing N N 306 NXD C9 H92 sing N N 307 NXD C9 H91 sing N N 308 NXD NAB CAC sing N N 309 NXD NAB HAB sing N N 310 NXD CAC OAD doub N N 311 NXD CAC CAF sing N N 312 NXD CAF OAG doub N N 313 NXD CAF NAK sing N N 314 NXD NAK HAK1 sing N N 315 NXD NAK HAK2 sing N N 316 PHE N CA sing N N 317 PHE N H sing N N 318 PHE N H2 sing N N 319 PHE CA C sing N N 320 PHE CA CB sing N N 321 PHE CA HA sing N N 322 PHE C O doub N N 323 PHE C OXT sing N N 324 PHE CB CG sing N N 325 PHE CB HB2 sing N N 326 PHE CB HB3 sing N N 327 PHE CG CD1 doub Y N 328 PHE CG CD2 sing Y N 329 PHE CD1 CE1 sing Y N 330 PHE CD1 HD1 sing N N 331 PHE CD2 CE2 doub Y N 332 PHE CD2 HD2 sing N N 333 PHE CE1 CZ doub Y N 334 PHE CE1 HE1 sing N N 335 PHE CE2 CZ sing Y N 336 PHE CE2 HE2 sing N N 337 PHE CZ HZ sing N N 338 PHE OXT HXT sing N N 339 PRO N CA sing N N 340 PRO N CD sing N N 341 PRO N H sing N N 342 PRO CA C sing N N 343 PRO CA CB sing N N 344 PRO CA HA sing N N 345 PRO C O doub N N 346 PRO C OXT sing N N 347 PRO CB CG sing N N 348 PRO CB HB2 sing N N 349 PRO CB HB3 sing N N 350 PRO CG CD sing N N 351 PRO CG HG2 sing N N 352 PRO CG HG3 sing N N 353 PRO CD HD2 sing N N 354 PRO CD HD3 sing N N 355 PRO OXT HXT sing N N 356 SER N CA sing N N 357 SER N H sing N N 358 SER N H2 sing N N 359 SER CA C sing N N 360 SER CA CB sing N N 361 SER CA HA sing N N 362 SER C O doub N N 363 SER C OXT sing N N 364 SER CB OG sing N N 365 SER CB HB2 sing N N 366 SER CB HB3 sing N N 367 SER OG HG sing N N 368 SER OXT HXT sing N N 369 THR N CA sing N N 370 THR N H sing N N 371 THR N H2 sing N N 372 THR CA C sing N N 373 THR CA CB sing N N 374 THR CA HA sing N N 375 THR C O doub N N 376 THR C OXT sing N N 377 THR CB OG1 sing N N 378 THR CB CG2 sing N N 379 THR CB HB sing N N 380 THR OG1 HG1 sing N N 381 THR CG2 HG21 sing N N 382 THR CG2 HG22 sing N N 383 THR CG2 HG23 sing N N 384 THR OXT HXT sing N N 385 TRP N CA sing N N 386 TRP N H sing N N 387 TRP N H2 sing N N 388 TRP CA C sing N N 389 TRP CA CB sing N N 390 TRP CA HA sing N N 391 TRP C O doub N N 392 TRP C OXT sing N N 393 TRP CB CG sing N N 394 TRP CB HB2 sing N N 395 TRP CB HB3 sing N N 396 TRP CG CD1 doub Y N 397 TRP CG CD2 sing Y N 398 TRP CD1 NE1 sing Y N 399 TRP CD1 HD1 sing N N 400 TRP CD2 CE2 doub Y N 401 TRP CD2 CE3 sing Y N 402 TRP NE1 CE2 sing Y N 403 TRP NE1 HE1 sing N N 404 TRP CE2 CZ2 sing Y N 405 TRP CE3 CZ3 doub Y N 406 TRP CE3 HE3 sing N N 407 TRP CZ2 CH2 doub Y N 408 TRP CZ2 HZ2 sing N N 409 TRP CZ3 CH2 sing Y N 410 TRP CZ3 HZ3 sing N N 411 TRP CH2 HH2 sing N N 412 TRP OXT HXT sing N N 413 TYR N CA sing N N 414 TYR N H sing N N 415 TYR N H2 sing N N 416 TYR CA C sing N N 417 TYR CA CB sing N N 418 TYR CA HA sing N N 419 TYR C O doub N N 420 TYR C OXT sing N N 421 TYR CB CG sing N N 422 TYR CB HB2 sing N N 423 TYR CB HB3 sing N N 424 TYR CG CD1 doub Y N 425 TYR CG CD2 sing Y N 426 TYR CD1 CE1 sing Y N 427 TYR CD1 HD1 sing N N 428 TYR CD2 CE2 doub Y N 429 TYR CD2 HD2 sing N N 430 TYR CE1 CZ doub Y N 431 TYR CE1 HE1 sing N N 432 TYR CE2 CZ sing Y N 433 TYR CE2 HE2 sing N N 434 TYR CZ OH sing N N 435 TYR OH HH sing N N 436 TYR OXT HXT sing N N 437 VAL N CA sing N N 438 VAL N H sing N N 439 VAL N H2 sing N N 440 VAL CA C sing N N 441 VAL CA CB sing N N 442 VAL CA HA sing N N 443 VAL C O doub N N 444 VAL C OXT sing N N 445 VAL CB CG1 sing N N 446 VAL CB CG2 sing N N 447 VAL CB HB sing N N 448 VAL CG1 HG11 sing N N 449 VAL CG1 HG12 sing N N 450 VAL CG1 HG13 sing N N 451 VAL CG2 HG21 sing N N 452 VAL CG2 HG22 sing N N 453 VAL CG2 HG23 sing N N 454 VAL OXT HXT sing N N 455 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 3 'methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' NXD 4 CYSTEINE CYS 5 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1O7S _pdbx_initial_refinement_model.details 'Siglec-7, APO, 1o7S' #