data_4AKM # _entry.id 4AKM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4AKM PDBE EBI-51448 WWPDB D_1290051448 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4AKM _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-02-24 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Krausze, J.' 1 'Wilke, S.' 2 'Buessow, K.' 3 # _citation.id primary _citation.title ;Crystal Structure of the Conserved Domain of the Dc Lysosomal Associated Membrane Protein: Implications for the Lysosomal Glycocalyx. ; _citation.journal_abbrev 'Bmc Biol.' _citation.journal_volume 10 _citation.page_first 62 _citation.page_last ? _citation.year 2012 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1741-7007 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22809326 _citation.pdbx_database_id_DOI 10.1186/1741-7007-10-62 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wilke, S.' 1 ? primary 'Krausze, J.' 2 ? primary 'Bussow, K.' 3 ? # _cell.entry_id 4AKM _cell.length_a 52.600 _cell.length_b 52.600 _cell.length_c 141.980 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AKM _symmetry.space_group_name_H-M 'P 31' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 # 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 'LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3' 18656.707 2 ? ? 'MEMBRANE-PROXIMAL PART OF LUMINAL DOMAIN, RESIDUES 222-381' ? 2 non-polymer syn 'IRIDIUM (III) ION' 192.217 4 ? ? ? ? 3 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 2 ? ? ? ? 4 water nat water 18.015 10 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;LAMP-3, LYSOSOMAL-ASSOCIATED MEMBRANE PROTEIN 3, DC-LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN, DC LAMP, PROTEIN TSC403, CD_ANTIGEN=CD208 ; # _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 ;SVKTGIYQVLNGSRLCIKAEMGIQLIVQDKESVFSPRRYFNIDPNATQASGNCGTRKSNLLLNFQGGFVNLTFTKDEESY YISEVGAYLTVSDPETVYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDECSSDYT HHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;SVKTGIYQVLNGSRLCIKAEMGIQLIVQDKESVFSPRRYFNIDPNATQASGNCGTRKSNLLLNFQGGFVNLTFTKDEESY YISEVGAYLTVSDPETVYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDECSSDYT HHHHHH ; _entity_poly.pdbx_strand_id A,B _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 SER n 1 2 VAL n 1 3 LYS n 1 4 THR n 1 5 GLY n 1 6 ILE n 1 7 TYR n 1 8 GLN n 1 9 VAL n 1 10 LEU n 1 11 ASN n 1 12 GLY n 1 13 SER n 1 14 ARG n 1 15 LEU n 1 16 CYS n 1 17 ILE n 1 18 LYS n 1 19 ALA n 1 20 GLU n 1 21 MET n 1 22 GLY n 1 23 ILE n 1 24 GLN n 1 25 LEU n 1 26 ILE n 1 27 VAL n 1 28 GLN n 1 29 ASP n 1 30 LYS n 1 31 GLU n 1 32 SER n 1 33 VAL n 1 34 PHE n 1 35 SER n 1 36 PRO n 1 37 ARG n 1 38 ARG n 1 39 TYR n 1 40 PHE n 1 41 ASN n 1 42 ILE n 1 43 ASP n 1 44 PRO n 1 45 ASN n 1 46 ALA n 1 47 THR n 1 48 GLN n 1 49 ALA n 1 50 SER n 1 51 GLY n 1 52 ASN n 1 53 CYS n 1 54 GLY n 1 55 THR n 1 56 ARG n 1 57 LYS n 1 58 SER n 1 59 ASN n 1 60 LEU n 1 61 LEU n 1 62 LEU n 1 63 ASN n 1 64 PHE n 1 65 GLN n 1 66 GLY n 1 67 GLY n 1 68 PHE n 1 69 VAL n 1 70 ASN n 1 71 LEU n 1 72 THR n 1 73 PHE n 1 74 THR n 1 75 LYS n 1 76 ASP n 1 77 GLU n 1 78 GLU n 1 79 SER n 1 80 TYR n 1 81 TYR n 1 82 ILE n 1 83 SER n 1 84 GLU n 1 85 VAL n 1 86 GLY n 1 87 ALA n 1 88 TYR n 1 89 LEU n 1 90 THR n 1 91 VAL n 1 92 SER n 1 93 ASP n 1 94 PRO n 1 95 GLU n 1 96 THR n 1 97 VAL n 1 98 TYR n 1 99 GLN n 1 100 GLY n 1 101 ILE n 1 102 LYS n 1 103 HIS n 1 104 ALA n 1 105 VAL n 1 106 VAL n 1 107 MET n 1 108 PHE n 1 109 GLN n 1 110 THR n 1 111 ALA n 1 112 VAL n 1 113 GLY n 1 114 HIS n 1 115 SER n 1 116 PHE n 1 117 LYS n 1 118 CYS n 1 119 VAL n 1 120 SER n 1 121 GLU n 1 122 GLN n 1 123 SER n 1 124 LEU n 1 125 GLN n 1 126 LEU n 1 127 SER n 1 128 ALA n 1 129 HIS n 1 130 LEU n 1 131 GLN n 1 132 VAL n 1 133 LYS n 1 134 THR n 1 135 THR n 1 136 ASP n 1 137 VAL n 1 138 GLN n 1 139 LEU n 1 140 GLN n 1 141 ALA n 1 142 PHE n 1 143 ASP n 1 144 PHE n 1 145 GLU n 1 146 ASP n 1 147 ASP n 1 148 HIS n 1 149 PHE n 1 150 GLY n 1 151 ASN n 1 152 VAL n 1 153 ASP n 1 154 GLU n 1 155 CYS n 1 156 SER n 1 157 SER n 1 158 ASP n 1 159 TYR n 1 160 THR n 1 161 HIS n 1 162 HIS n 1 163 HIS n 1 164 HIS n 1 165 HIS n 1 166 HIS 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 ? _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 ? _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 'CHO LEC3.2.8.1' _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code LAMP3_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession Q9UQV4 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4AKM A 1 ? 160 ? Q9UQV4 222 ? 381 ? 222 381 2 1 4AKM B 1 ? 160 ? Q9UQV4 222 ? 381 ? 222 381 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4AKM HIS A 161 ? UNP Q9UQV4 ? ? 'expression tag' 382 1 1 4AKM HIS A 162 ? UNP Q9UQV4 ? ? 'expression tag' 383 2 1 4AKM HIS A 163 ? UNP Q9UQV4 ? ? 'expression tag' 384 3 1 4AKM HIS A 164 ? UNP Q9UQV4 ? ? 'expression tag' 385 4 1 4AKM HIS A 165 ? UNP Q9UQV4 ? ? 'expression tag' 386 5 1 4AKM HIS A 166 ? UNP Q9UQV4 ? ? 'expression tag' 387 6 1 4AKM VAL A 97 ? UNP Q9UQV4 ILE 318 variant 318 7 2 4AKM HIS B 161 ? UNP Q9UQV4 ? ? 'expression tag' 382 8 2 4AKM HIS B 162 ? UNP Q9UQV4 ? ? 'expression tag' 383 9 2 4AKM HIS B 163 ? UNP Q9UQV4 ? ? 'expression tag' 384 10 2 4AKM HIS B 164 ? UNP Q9UQV4 ? ? 'expression tag' 385 11 2 4AKM HIS B 165 ? UNP Q9UQV4 ? ? 'expression tag' 386 12 2 4AKM HIS B 166 ? UNP Q9UQV4 ? ? 'expression tag' 387 13 2 4AKM VAL B 97 ? UNP Q9UQV4 ILE 318 variant 318 14 # 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 IR3 non-polymer . 'IRIDIUM (III) ION' ? 'Ir 3' 192.217 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 ? 'C8 H15 N O6' 221.208 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 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 4AKM _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.28 _exptl_crystal.density_percent_sol 62.5 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;PROTEIN WAS CRYSTALLIZED FROM 5% PEG 6000, 0.1 M CITRIC ACID, PH 5.0; THEN SOAKED IN 0.014 M AMMONIUM HEXACHLOROIRIDATE(III)HYDRATE AND CRYO-PROTECTED IN 30% PEG 6000. ; # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 2010-05-07 _diffrn_detector.details MIRROR # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SI(111)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.10371 1.0 2 1.1042 1.0 3 1.1009 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X12' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X12 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.10371, 1.1042, 1.1009' # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4AKM _reflns.observed_criterion_sigma_I 2.5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.00 _reflns.d_resolution_high 2.70 _reflns.number_obs 11238 _reflns.number_all ? _reflns.percent_possible_obs 91.1 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.48 _reflns.B_iso_Wilson_estimate 55.49 _reflns.pdbx_redundancy 2.86 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.70 _reflns_shell.d_res_low 2.85 _reflns_shell.percent_possible_all 97.9 _reflns_shell.Rmerge_I_obs 0.46 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.47 _reflns_shell.pdbx_redundancy 2.84 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4AKM _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 11232 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.98 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.295 _refine.ls_d_res_high 2.687 _refine.ls_percent_reflns_obs 92.05 _refine.ls_R_factor_obs 0.2277 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2265 _refine.ls_R_factor_R_free 0.2492 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 562 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 61.3 _refine.aniso_B[1][1] 6.4177 _refine.aniso_B[2][2] 6.4177 _refine.aniso_B[3][3] -12.8354 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.235 _refine.solvent_model_param_bsol 10.238 _refine.pdbx_solvent_vdw_probe_radii 1.30 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 1.11 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values MLHL _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.87 _refine.pdbx_overall_phase_error 29.06 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _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 2438 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 32 _refine_hist.number_atoms_solvent 10 _refine_hist.number_atoms_total 2480 _refine_hist.d_res_high 2.687 _refine_hist.d_res_low 19.295 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.006 ? ? 2516 'X-RAY DIFFRACTION' ? f_angle_d 1.023 ? ? 3394 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 26.206 ? ? 1528 'X-RAY DIFFRACTION' ? f_chiral_restr 0.073 ? ? 386 'X-RAY DIFFRACTION' ? f_plane_restr 0.003 ? ? 442 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.6873 2.9569 2885 0.3261 99.00 0.3637 . . 151 . . 'X-RAY DIFFRACTION' . 2.9569 3.3828 2878 0.2760 100.00 0.3530 . . 152 . . 'X-RAY DIFFRACTION' . 3.3828 4.2544 1988 0.2186 69.00 0.2784 . . 105 . . 'X-RAY DIFFRACTION' . 4.2544 19.2959 2919 0.1895 100.00 0.1783 . . 154 . . # _struct_ncs_oper.id 1 _struct_ncs_oper.code given _struct_ncs_oper.details ? _struct_ncs_oper.matrix[1][1] 0.929100 _struct_ncs_oper.matrix[1][2] 0.357590 _struct_ncs_oper.matrix[1][3] 0.094370 _struct_ncs_oper.matrix[2][1] 0.355850 _struct_ncs_oper.matrix[2][2] -0.933880 _struct_ncs_oper.matrix[2][3] 0.035260 _struct_ncs_oper.matrix[3][1] 0.100740 _struct_ncs_oper.matrix[3][2] 0.000820 _struct_ncs_oper.matrix[3][3] -0.994910 _struct_ncs_oper.vector[1] -11.62670 _struct_ncs_oper.vector[2] 17.47254 _struct_ncs_oper.vector[3] 153.64288 # _struct.entry_id 4AKM _struct.title 'Crystal structure of the human lysosome-associated membrane protein LAMP-3 (aka DC-LAMP)' _struct.pdbx_descriptor 'LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4AKM _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' _struct_keywords.text 'MEMBRANE PROTEIN, GLYCOSYLATION, BETA PRISM' # 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 1 ? C N N 2 ? D N N 3 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 2 ? I N N 4 ? J N N 4 ? # _struct_biol.id 1 # 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 43 ? THR A 47 ? ASP A 264 THR A 268 5 ? 5 HELX_P HELX_P2 2 ASP B 43 ? ASN B 45 ? ASP B 264 ASN B 266 5 ? 3 # _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 ? ? A CYS 16 SG ? ? ? 1_555 A CYS 53 SG ? ? A CYS 237 A CYS 274 1_555 ? ? ? ? ? ? ? 2.047 ? ? disulf2 disulf ? ? A CYS 118 SG ? ? ? 1_555 A CYS 155 SG ? ? A CYS 339 A CYS 376 1_555 ? ? ? ? ? ? ? 2.026 ? ? disulf3 disulf ? ? B CYS 16 SG ? ? ? 1_555 B CYS 53 SG ? ? B CYS 237 B CYS 274 1_555 ? ? ? ? ? ? ? 2.041 ? ? disulf4 disulf ? ? B CYS 118 SG ? ? ? 1_555 B CYS 155 SG ? ? B CYS 339 B CYS 376 1_555 ? ? ? ? ? ? ? 2.054 ? ? covale1 covale one ? A ASN 70 ND2 ? ? ? 1_555 D NAG . C1 ? ? A ASN 291 A NAG 1379 1_555 ? ? ? ? ? ? ? 1.437 ? N-Glycosylation covale2 covale one ? B ASN 70 ND2 ? ? ? 1_555 G NAG . C1 ? ? B ASN 291 B NAG 1380 1_555 ? ? ? ? ? ? ? 1.438 ? N-Glycosylation # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLU 77 A . ? GLU 298 A GLU 78 A ? GLU 299 A 1 -5.82 2 ASP 93 A . ? ASP 314 A PRO 94 A ? PRO 315 A 1 1.51 3 SER 1 B . ? SER 222 B VAL 2 B ? VAL 223 B 1 -0.12 4 GLU 77 B . ? GLU 298 B GLU 78 B ? GLU 299 B 1 -1.06 5 ASP 93 B . ? ASP 314 B PRO 94 B ? PRO 315 B 1 -10.86 6 SER 156 B . ? SER 377 B SER 157 B ? SER 378 B 1 -4.28 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 2 ? AC ? 2 ? AD ? 2 ? AE ? 5 ? AF ? 5 ? AG ? 2 ? BA ? 2 ? BB ? 2 ? BC ? 2 ? BD ? 4 ? BE ? 5 ? BF ? 5 ? BG ? 5 ? BH ? 2 ? # 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 AA 1 2 ? anti-parallel AB 1 2 ? parallel AC 1 2 ? anti-parallel AD 1 2 ? parallel AE 1 2 ? anti-parallel AE 2 3 ? anti-parallel AE 3 4 ? anti-parallel AE 4 5 ? anti-parallel AF 1 2 ? anti-parallel AF 2 3 ? anti-parallel AF 3 4 ? anti-parallel AF 4 5 ? anti-parallel AG 1 2 ? anti-parallel BA 1 2 ? anti-parallel BB 1 2 ? parallel BC 1 2 ? parallel BD 1 2 ? parallel BD 2 3 ? anti-parallel BD 3 4 ? parallel BE 1 2 ? parallel BE 2 3 ? anti-parallel BE 3 4 ? anti-parallel BE 4 5 ? parallel BF 1 2 ? anti-parallel BF 2 3 ? anti-parallel BF 3 4 ? anti-parallel BF 4 5 ? anti-parallel BG 1 2 ? anti-parallel BG 2 3 ? anti-parallel BG 3 4 ? anti-parallel BG 4 5 ? anti-parallel BH 1 2 ? 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 AA 1 GLY A 5 ? ASN A 11 ? GLY A 226 ASN A 232 AA 2 ARG A 14 ? VAL A 27 ? ARG A 235 VAL A 248 AB 1 ARG A 38 ? ASN A 41 ? ARG A 259 ASN A 262 AB 2 ARG A 14 ? VAL A 27 ? ARG A 235 VAL A 248 AC 1 PHE A 116 ? CYS A 118 ? PHE A 337 CYS A 339 AC 2 LEU A 130 ? ALA A 141 ? LEU A 351 ALA A 362 AD 1 GLN A 122 ? GLN A 125 ? GLN A 343 GLN A 346 AD 2 LEU A 130 ? ALA A 141 ? LEU A 351 ALA A 362 AE 1 GLN A 48 ? ASN A 52 ? GLN A 269 ASN A 273 AE 2 LYS A 57 ? PHE A 64 ? LYS A 278 PHE A 285 AE 3 GLY A 67 ? LYS A 75 ? GLY A 288 LYS A 296 AE 4 TYR A 80 ? THR A 90 ? TYR A 301 THR A 311 AE 5 VAL A 97 ? LYS A 102 ? VAL A 318 LYS A 323 AF 1 GLN A 48 ? ASN A 52 ? GLN A 269 ASN A 273 AF 2 LYS A 57 ? PHE A 64 ? LYS A 278 PHE A 285 AF 3 GLY A 67 ? LYS A 75 ? GLY A 288 LYS A 296 AF 4 TYR A 80 ? THR A 90 ? TYR A 301 THR A 311 AF 5 MET A 107 ? THR A 110 ? MET A 328 THR A 331 AG 1 VAL A 97 ? LYS A 102 ? VAL A 318 LYS A 323 AG 2 TYR A 80 ? THR A 90 ? TYR A 301 THR A 311 BA 1 GLY B 5 ? ASN B 11 ? GLY B 226 ASN B 232 BA 2 ARG B 14 ? GLN B 28 ? ARG B 235 GLN B 249 BB 1 ARG B 37 ? ASN B 41 ? ARG B 258 ASN B 262 BB 2 ARG B 14 ? GLN B 28 ? ARG B 235 GLN B 249 BC 1 GLN B 122 ? GLN B 125 ? GLN B 343 GLN B 346 BC 2 LEU B 130 ? ALA B 141 ? LEU B 351 ALA B 362 BD 1 VAL B 152 ? GLU B 154 ? VAL B 373 GLU B 375 BD 2 SER B 115 ? CYS B 118 ? SER B 336 CYS B 339 BD 3 LEU B 130 ? ALA B 141 ? LEU B 351 ALA B 362 BD 4 GLN B 122 ? GLN B 125 ? GLN B 343 GLN B 346 BE 1 VAL B 152 ? GLU B 154 ? VAL B 373 GLU B 375 BE 2 SER B 115 ? CYS B 118 ? SER B 336 CYS B 339 BE 3 LEU B 130 ? ALA B 141 ? LEU B 351 ALA B 362 BE 4 ARG B 14 ? GLN B 28 ? ARG B 235 GLN B 249 BE 5 ARG B 37 ? ASN B 41 ? ARG B 258 ASN B 262 BF 1 THR B 47 ? SER B 50 ? THR B 268 SER B 271 BF 2 LYS B 57 ? PHE B 64 ? LYS B 278 PHE B 285 BF 3 GLY B 67 ? LYS B 75 ? GLY B 288 LYS B 296 BF 4 SER B 79 ? VAL B 91 ? SER B 300 VAL B 312 BF 5 THR B 96 ? LYS B 102 ? THR B 317 LYS B 323 BG 1 THR B 47 ? SER B 50 ? THR B 268 SER B 271 BG 2 LYS B 57 ? PHE B 64 ? LYS B 278 PHE B 285 BG 3 GLY B 67 ? LYS B 75 ? GLY B 288 LYS B 296 BG 4 SER B 79 ? VAL B 91 ? SER B 300 VAL B 312 BG 5 MET B 107 ? ALA B 111 ? MET B 328 ALA B 332 BH 1 THR B 96 ? LYS B 102 ? THR B 317 LYS B 323 BH 2 SER B 79 ? VAL B 91 ? SER B 300 VAL B 312 # 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 AA 1 2 N ASN A 11 ? N ASN A 232 O ARG A 14 ? O ARG A 235 AB 1 2 N PHE A 40 ? N PHE A 261 O LEU A 25 ? O LEU A 246 AC 1 2 N CYS A 118 ? N CYS A 339 O VAL A 137 ? O VAL A 358 AD 1 2 N LEU A 124 ? N LEU A 345 O VAL A 132 ? O VAL A 353 AE 1 2 N ASN A 52 ? N ASN A 273 O ASN A 59 ? O ASN A 280 AE 2 3 N PHE A 64 ? N PHE A 285 O GLY A 67 ? O GLY A 288 AE 3 4 N THR A 74 ? N THR A 295 O TYR A 81 ? O TYR A 302 AE 4 5 N LEU A 89 ? N LEU A 310 O TYR A 98 ? O TYR A 319 AF 1 2 N ASN A 52 ? N ASN A 273 O ASN A 59 ? O ASN A 280 AF 2 3 N PHE A 64 ? N PHE A 285 O GLY A 67 ? O GLY A 288 AF 3 4 N THR A 74 ? N THR A 295 O TYR A 81 ? O TYR A 302 AF 4 5 N ILE A 82 ? N ILE A 303 O MET A 107 ? O MET A 328 AG 1 2 N LYS A 102 ? N LYS A 323 O VAL A 85 ? O VAL A 306 BA 1 2 N ASN B 11 ? N ASN B 232 O ARG B 14 ? O ARG B 235 BB 1 2 N PHE B 40 ? N PHE B 261 O LEU B 25 ? O LEU B 246 BC 1 2 N LEU B 124 ? N LEU B 345 O VAL B 132 ? O VAL B 353 BD 1 2 N ASP B 153 ? N ASP B 374 O SER B 115 ? O SER B 336 BD 2 3 N CYS B 118 ? N CYS B 339 O VAL B 137 ? O VAL B 358 BD 3 4 N THR B 134 ? N THR B 355 O GLN B 122 ? O GLN B 343 BE 1 2 N ASP B 153 ? N ASP B 374 O SER B 115 ? O SER B 336 BE 2 3 N CYS B 118 ? N CYS B 339 O VAL B 137 ? O VAL B 358 BE 3 4 N GLN B 140 ? N GLN B 361 O LYS B 18 ? O LYS B 239 BE 4 5 N VAL B 27 ? N VAL B 248 O ARG B 38 ? O ARG B 259 BF 1 2 N SER B 50 ? N SER B 271 O LEU B 61 ? O LEU B 282 BF 2 3 N PHE B 64 ? N PHE B 285 O GLY B 67 ? O GLY B 288 BF 3 4 N THR B 74 ? N THR B 295 O TYR B 81 ? O TYR B 302 BF 4 5 N VAL B 91 ? N VAL B 312 O THR B 96 ? O THR B 317 BG 1 2 N SER B 50 ? N SER B 271 O LEU B 61 ? O LEU B 282 BG 2 3 N PHE B 64 ? N PHE B 285 O GLY B 67 ? O GLY B 288 BG 3 4 N THR B 74 ? N THR B 295 O TYR B 81 ? O TYR B 302 BG 4 5 N ILE B 82 ? N ILE B 303 O MET B 107 ? O MET B 328 BH 1 2 N LYS B 102 ? N LYS B 323 O VAL B 85 ? O VAL B 306 # _database_PDB_matrix.entry_id 4AKM _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4AKM _atom_sites.fract_transf_matrix[1][1] 0.019011 _atom_sites.fract_transf_matrix[1][2] 0.010976 _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] 0.021952 _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] 0.007043 _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 IR 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 SER 1 222 ? ? ? A . n A 1 2 VAL 2 223 223 VAL VAL A . n A 1 3 LYS 3 224 224 LYS LYS A . n A 1 4 THR 4 225 225 THR THR A . n A 1 5 GLY 5 226 226 GLY GLY A . n A 1 6 ILE 6 227 227 ILE ILE A . n A 1 7 TYR 7 228 228 TYR TYR A . n A 1 8 GLN 8 229 229 GLN GLN A . n A 1 9 VAL 9 230 230 VAL VAL A . n A 1 10 LEU 10 231 231 LEU LEU A . n A 1 11 ASN 11 232 232 ASN ASN A . n A 1 12 GLY 12 233 233 GLY GLY A . n A 1 13 SER 13 234 234 SER SER A . n A 1 14 ARG 14 235 235 ARG ARG A . n A 1 15 LEU 15 236 236 LEU LEU A . n A 1 16 CYS 16 237 237 CYS CYS A . n A 1 17 ILE 17 238 238 ILE ILE A . n A 1 18 LYS 18 239 239 LYS LYS A . n A 1 19 ALA 19 240 240 ALA ALA A . n A 1 20 GLU 20 241 241 GLU GLU A . n A 1 21 MET 21 242 242 MET MET A . n A 1 22 GLY 22 243 243 GLY GLY A . n A 1 23 ILE 23 244 244 ILE ILE A . n A 1 24 GLN 24 245 245 GLN GLN A . n A 1 25 LEU 25 246 246 LEU LEU A . n A 1 26 ILE 26 247 247 ILE ILE A . n A 1 27 VAL 27 248 248 VAL VAL A . n A 1 28 GLN 28 249 249 GLN GLN A . n A 1 29 ASP 29 250 250 ASP ASP A . n A 1 30 LYS 30 251 251 LYS LYS A . n A 1 31 GLU 31 252 252 GLU GLU A . n A 1 32 SER 32 253 253 SER SER A . n A 1 33 VAL 33 254 254 VAL VAL A . n A 1 34 PHE 34 255 255 PHE PHE A . n A 1 35 SER 35 256 256 SER SER A . n A 1 36 PRO 36 257 257 PRO PRO A . n A 1 37 ARG 37 258 258 ARG ARG A . n A 1 38 ARG 38 259 259 ARG ARG A . n A 1 39 TYR 39 260 260 TYR TYR A . n A 1 40 PHE 40 261 261 PHE PHE A . n A 1 41 ASN 41 262 262 ASN ASN A . n A 1 42 ILE 42 263 263 ILE ILE A . n A 1 43 ASP 43 264 264 ASP ASP A . n A 1 44 PRO 44 265 265 PRO PRO A . n A 1 45 ASN 45 266 266 ASN ASN A . n A 1 46 ALA 46 267 267 ALA ALA A . n A 1 47 THR 47 268 268 THR THR A . n A 1 48 GLN 48 269 269 GLN GLN A . n A 1 49 ALA 49 270 270 ALA ALA A . n A 1 50 SER 50 271 271 SER SER A . n A 1 51 GLY 51 272 272 GLY GLY A . n A 1 52 ASN 52 273 273 ASN ASN A . n A 1 53 CYS 53 274 274 CYS CYS A . n A 1 54 GLY 54 275 275 GLY GLY A . n A 1 55 THR 55 276 276 THR THR A . n A 1 56 ARG 56 277 277 ARG ARG A . n A 1 57 LYS 57 278 278 LYS LYS A . n A 1 58 SER 58 279 279 SER SER A . n A 1 59 ASN 59 280 280 ASN ASN A . n A 1 60 LEU 60 281 281 LEU LEU A . n A 1 61 LEU 61 282 282 LEU LEU A . n A 1 62 LEU 62 283 283 LEU LEU A . n A 1 63 ASN 63 284 284 ASN ASN A . n A 1 64 PHE 64 285 285 PHE PHE A . n A 1 65 GLN 65 286 286 GLN GLN A . n A 1 66 GLY 66 287 287 GLY GLY A . n A 1 67 GLY 67 288 288 GLY GLY A . n A 1 68 PHE 68 289 289 PHE PHE A . n A 1 69 VAL 69 290 290 VAL VAL A . n A 1 70 ASN 70 291 291 ASN ASN A . n A 1 71 LEU 71 292 292 LEU LEU A . n A 1 72 THR 72 293 293 THR THR A . n A 1 73 PHE 73 294 294 PHE PHE A . n A 1 74 THR 74 295 295 THR THR A . n A 1 75 LYS 75 296 296 LYS LYS A . n A 1 76 ASP 76 297 297 ASP ASP A . n A 1 77 GLU 77 298 298 GLU GLU A . n A 1 78 GLU 78 299 299 GLU GLU A . n A 1 79 SER 79 300 300 SER SER A . n A 1 80 TYR 80 301 301 TYR TYR A . n A 1 81 TYR 81 302 302 TYR TYR A . n A 1 82 ILE 82 303 303 ILE ILE A . n A 1 83 SER 83 304 304 SER SER A . n A 1 84 GLU 84 305 305 GLU GLU A . n A 1 85 VAL 85 306 306 VAL VAL A . n A 1 86 GLY 86 307 307 GLY GLY A . n A 1 87 ALA 87 308 308 ALA ALA A . n A 1 88 TYR 88 309 309 TYR TYR A . n A 1 89 LEU 89 310 310 LEU LEU A . n A 1 90 THR 90 311 311 THR THR A . n A 1 91 VAL 91 312 312 VAL VAL A . n A 1 92 SER 92 313 313 SER SER A . n A 1 93 ASP 93 314 314 ASP ASP A . n A 1 94 PRO 94 315 315 PRO PRO A . n A 1 95 GLU 95 316 316 GLU GLU A . n A 1 96 THR 96 317 317 THR THR A . n A 1 97 VAL 97 318 318 VAL VAL A . n A 1 98 TYR 98 319 319 TYR TYR A . n A 1 99 GLN 99 320 320 GLN GLN A . n A 1 100 GLY 100 321 321 GLY GLY A . n A 1 101 ILE 101 322 322 ILE ILE A . n A 1 102 LYS 102 323 323 LYS LYS A . n A 1 103 HIS 103 324 324 HIS HIS A . n A 1 104 ALA 104 325 325 ALA ALA A . n A 1 105 VAL 105 326 326 VAL VAL A . n A 1 106 VAL 106 327 327 VAL VAL A . n A 1 107 MET 107 328 328 MET MET A . n A 1 108 PHE 108 329 329 PHE PHE A . n A 1 109 GLN 109 330 330 GLN GLN A . n A 1 110 THR 110 331 331 THR THR A . n A 1 111 ALA 111 332 332 ALA ALA A . n A 1 112 VAL 112 333 333 VAL VAL A . n A 1 113 GLY 113 334 334 GLY GLY A . n A 1 114 HIS 114 335 335 HIS HIS A . n A 1 115 SER 115 336 336 SER SER A . n A 1 116 PHE 116 337 337 PHE PHE A . n A 1 117 LYS 117 338 338 LYS LYS A . n A 1 118 CYS 118 339 339 CYS CYS A . n A 1 119 VAL 119 340 340 VAL VAL A . n A 1 120 SER 120 341 341 SER SER A . n A 1 121 GLU 121 342 342 GLU GLU A . n A 1 122 GLN 122 343 343 GLN GLN A . n A 1 123 SER 123 344 344 SER SER A . n A 1 124 LEU 124 345 345 LEU LEU A . n A 1 125 GLN 125 346 346 GLN GLN A . n A 1 126 LEU 126 347 347 LEU LEU A . n A 1 127 SER 127 348 348 SER SER A . n A 1 128 ALA 128 349 349 ALA ALA A . n A 1 129 HIS 129 350 350 HIS HIS A . n A 1 130 LEU 130 351 351 LEU LEU A . n A 1 131 GLN 131 352 352 GLN GLN A . n A 1 132 VAL 132 353 353 VAL VAL A . n A 1 133 LYS 133 354 354 LYS LYS A . n A 1 134 THR 134 355 355 THR THR A . n A 1 135 THR 135 356 356 THR THR A . n A 1 136 ASP 136 357 357 ASP ASP A . n A 1 137 VAL 137 358 358 VAL VAL A . n A 1 138 GLN 138 359 359 GLN GLN A . n A 1 139 LEU 139 360 360 LEU LEU A . n A 1 140 GLN 140 361 361 GLN GLN A . n A 1 141 ALA 141 362 362 ALA ALA A . n A 1 142 PHE 142 363 363 PHE PHE A . n A 1 143 ASP 143 364 364 ASP ASP A . n A 1 144 PHE 144 365 365 PHE PHE A . n A 1 145 GLU 145 366 366 GLU GLU A . n A 1 146 ASP 146 367 367 ASP ASP A . n A 1 147 ASP 147 368 368 ASP ASP A . n A 1 148 HIS 148 369 369 HIS HIS A . n A 1 149 PHE 149 370 370 PHE PHE A . n A 1 150 GLY 150 371 371 GLY GLY A . n A 1 151 ASN 151 372 372 ASN ASN A . n A 1 152 VAL 152 373 373 VAL VAL A . n A 1 153 ASP 153 374 374 ASP ASP A . n A 1 154 GLU 154 375 375 GLU GLU A . n A 1 155 CYS 155 376 376 CYS CYS A . n A 1 156 SER 156 377 377 SER SER A . n A 1 157 SER 157 378 ? ? ? A . n A 1 158 ASP 158 379 ? ? ? A . n A 1 159 TYR 159 380 ? ? ? A . n A 1 160 THR 160 381 ? ? ? A . n A 1 161 HIS 161 382 ? ? ? A . n A 1 162 HIS 162 383 ? ? ? A . n A 1 163 HIS 163 384 ? ? ? A . n A 1 164 HIS 164 385 ? ? ? A . n A 1 165 HIS 165 386 ? ? ? A . n A 1 166 HIS 166 387 ? ? ? A . n B 1 1 SER 1 222 222 SER SER B . n B 1 2 VAL 2 223 223 VAL VAL B . n B 1 3 LYS 3 224 224 LYS LYS B . n B 1 4 THR 4 225 225 THR THR B . n B 1 5 GLY 5 226 226 GLY GLY B . n B 1 6 ILE 6 227 227 ILE ILE B . n B 1 7 TYR 7 228 228 TYR TYR B . n B 1 8 GLN 8 229 229 GLN GLN B . n B 1 9 VAL 9 230 230 VAL VAL B . n B 1 10 LEU 10 231 231 LEU LEU B . n B 1 11 ASN 11 232 232 ASN ASN B . n B 1 12 GLY 12 233 233 GLY GLY B . n B 1 13 SER 13 234 234 SER SER B . n B 1 14 ARG 14 235 235 ARG ARG B . n B 1 15 LEU 15 236 236 LEU LEU B . n B 1 16 CYS 16 237 237 CYS CYS B . n B 1 17 ILE 17 238 238 ILE ILE B . n B 1 18 LYS 18 239 239 LYS LYS B . n B 1 19 ALA 19 240 240 ALA ALA B . n B 1 20 GLU 20 241 241 GLU GLU B . n B 1 21 MET 21 242 242 MET MET B . n B 1 22 GLY 22 243 243 GLY GLY B . n B 1 23 ILE 23 244 244 ILE ILE B . n B 1 24 GLN 24 245 245 GLN GLN B . n B 1 25 LEU 25 246 246 LEU LEU B . n B 1 26 ILE 26 247 247 ILE ILE B . n B 1 27 VAL 27 248 248 VAL VAL B . n B 1 28 GLN 28 249 249 GLN GLN B . n B 1 29 ASP 29 250 250 ASP ASP B . n B 1 30 LYS 30 251 251 LYS LYS B . n B 1 31 GLU 31 252 252 GLU GLU B . n B 1 32 SER 32 253 253 SER SER B . n B 1 33 VAL 33 254 254 VAL VAL B . n B 1 34 PHE 34 255 255 PHE PHE B . n B 1 35 SER 35 256 256 SER SER B . n B 1 36 PRO 36 257 257 PRO PRO B . n B 1 37 ARG 37 258 258 ARG ARG B . n B 1 38 ARG 38 259 259 ARG ARG B . n B 1 39 TYR 39 260 260 TYR TYR B . n B 1 40 PHE 40 261 261 PHE PHE B . n B 1 41 ASN 41 262 262 ASN ASN B . n B 1 42 ILE 42 263 263 ILE ILE B . n B 1 43 ASP 43 264 264 ASP ASP B . n B 1 44 PRO 44 265 265 PRO PRO B . n B 1 45 ASN 45 266 266 ASN ASN B . n B 1 46 ALA 46 267 267 ALA ALA B . n B 1 47 THR 47 268 268 THR THR B . n B 1 48 GLN 48 269 269 GLN GLN B . n B 1 49 ALA 49 270 270 ALA ALA B . n B 1 50 SER 50 271 271 SER SER B . n B 1 51 GLY 51 272 272 GLY GLY B . n B 1 52 ASN 52 273 273 ASN ASN B . n B 1 53 CYS 53 274 274 CYS CYS B . n B 1 54 GLY 54 275 275 GLY GLY B . n B 1 55 THR 55 276 276 THR THR B . n B 1 56 ARG 56 277 277 ARG ARG B . n B 1 57 LYS 57 278 278 LYS LYS B . n B 1 58 SER 58 279 279 SER SER B . n B 1 59 ASN 59 280 280 ASN ASN B . n B 1 60 LEU 60 281 281 LEU LEU B . n B 1 61 LEU 61 282 282 LEU LEU B . n B 1 62 LEU 62 283 283 LEU LEU B . n B 1 63 ASN 63 284 284 ASN ASN B . n B 1 64 PHE 64 285 285 PHE PHE B . n B 1 65 GLN 65 286 286 GLN GLN B . n B 1 66 GLY 66 287 287 GLY GLY B . n B 1 67 GLY 67 288 288 GLY GLY B . n B 1 68 PHE 68 289 289 PHE PHE B . n B 1 69 VAL 69 290 290 VAL VAL B . n B 1 70 ASN 70 291 291 ASN ASN B . n B 1 71 LEU 71 292 292 LEU LEU B . n B 1 72 THR 72 293 293 THR THR B . n B 1 73 PHE 73 294 294 PHE PHE B . n B 1 74 THR 74 295 295 THR THR B . n B 1 75 LYS 75 296 296 LYS LYS B . n B 1 76 ASP 76 297 297 ASP ASP B . n B 1 77 GLU 77 298 298 GLU GLU B . n B 1 78 GLU 78 299 299 GLU GLU B . n B 1 79 SER 79 300 300 SER SER B . n B 1 80 TYR 80 301 301 TYR TYR B . n B 1 81 TYR 81 302 302 TYR TYR B . n B 1 82 ILE 82 303 303 ILE ILE B . n B 1 83 SER 83 304 304 SER SER B . n B 1 84 GLU 84 305 305 GLU GLU B . n B 1 85 VAL 85 306 306 VAL VAL B . n B 1 86 GLY 86 307 307 GLY GLY B . n B 1 87 ALA 87 308 308 ALA ALA B . n B 1 88 TYR 88 309 309 TYR TYR B . n B 1 89 LEU 89 310 310 LEU LEU B . n B 1 90 THR 90 311 311 THR THR B . n B 1 91 VAL 91 312 312 VAL VAL B . n B 1 92 SER 92 313 313 SER SER B . n B 1 93 ASP 93 314 314 ASP ASP B . n B 1 94 PRO 94 315 315 PRO PRO B . n B 1 95 GLU 95 316 316 GLU GLU B . n B 1 96 THR 96 317 317 THR THR B . n B 1 97 VAL 97 318 318 VAL VAL B . n B 1 98 TYR 98 319 319 TYR TYR B . n B 1 99 GLN 99 320 320 GLN GLN B . n B 1 100 GLY 100 321 321 GLY GLY B . n B 1 101 ILE 101 322 322 ILE ILE B . n B 1 102 LYS 102 323 323 LYS LYS B . n B 1 103 HIS 103 324 324 HIS HIS B . n B 1 104 ALA 104 325 325 ALA ALA B . n B 1 105 VAL 105 326 326 VAL VAL B . n B 1 106 VAL 106 327 327 VAL VAL B . n B 1 107 MET 107 328 328 MET MET B . n B 1 108 PHE 108 329 329 PHE PHE B . n B 1 109 GLN 109 330 330 GLN GLN B . n B 1 110 THR 110 331 331 THR THR B . n B 1 111 ALA 111 332 332 ALA ALA B . n B 1 112 VAL 112 333 333 VAL VAL B . n B 1 113 GLY 113 334 334 GLY GLY B . n B 1 114 HIS 114 335 335 HIS HIS B . n B 1 115 SER 115 336 336 SER SER B . n B 1 116 PHE 116 337 337 PHE PHE B . n B 1 117 LYS 117 338 338 LYS LYS B . n B 1 118 CYS 118 339 339 CYS CYS B . n B 1 119 VAL 119 340 340 VAL VAL B . n B 1 120 SER 120 341 341 SER SER B . n B 1 121 GLU 121 342 342 GLU GLU B . n B 1 122 GLN 122 343 343 GLN GLN B . n B 1 123 SER 123 344 344 SER SER B . n B 1 124 LEU 124 345 345 LEU LEU B . n B 1 125 GLN 125 346 346 GLN GLN B . n B 1 126 LEU 126 347 347 LEU LEU B . n B 1 127 SER 127 348 348 SER SER B . n B 1 128 ALA 128 349 349 ALA ALA B . n B 1 129 HIS 129 350 350 HIS HIS B . n B 1 130 LEU 130 351 351 LEU LEU B . n B 1 131 GLN 131 352 352 GLN GLN B . n B 1 132 VAL 132 353 353 VAL VAL B . n B 1 133 LYS 133 354 354 LYS LYS B . n B 1 134 THR 134 355 355 THR THR B . n B 1 135 THR 135 356 356 THR THR B . n B 1 136 ASP 136 357 357 ASP ASP B . n B 1 137 VAL 137 358 358 VAL VAL B . n B 1 138 GLN 138 359 359 GLN GLN B . n B 1 139 LEU 139 360 360 LEU LEU B . n B 1 140 GLN 140 361 361 GLN GLN B . n B 1 141 ALA 141 362 362 ALA ALA B . n B 1 142 PHE 142 363 363 PHE PHE B . n B 1 143 ASP 143 364 364 ASP ASP B . n B 1 144 PHE 144 365 365 PHE PHE B . n B 1 145 GLU 145 366 366 GLU GLU B . n B 1 146 ASP 146 367 367 ASP ASP B . n B 1 147 ASP 147 368 368 ASP ASP B . n B 1 148 HIS 148 369 369 HIS HIS B . n B 1 149 PHE 149 370 370 PHE PHE B . n B 1 150 GLY 150 371 371 GLY GLY B . n B 1 151 ASN 151 372 372 ASN ASN B . n B 1 152 VAL 152 373 373 VAL VAL B . n B 1 153 ASP 153 374 374 ASP ASP B . n B 1 154 GLU 154 375 375 GLU GLU B . n B 1 155 CYS 155 376 376 CYS CYS B . n B 1 156 SER 156 377 377 SER SER B . n B 1 157 SER 157 378 378 SER SER B . n B 1 158 ASP 158 379 ? ? ? B . n B 1 159 TYR 159 380 ? ? ? B . n B 1 160 THR 160 381 ? ? ? B . n B 1 161 HIS 161 382 ? ? ? B . n B 1 162 HIS 162 383 ? ? ? B . n B 1 163 HIS 163 384 ? ? ? B . n B 1 164 HIS 164 385 ? ? ? B . n B 1 165 HIS 165 386 ? ? ? B . n B 1 166 HIS 166 387 ? ? ? B . 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 C 2 IR3 1 1378 1378 IR3 IR3 A . D 3 NAG 1 1379 1379 NAG NAG A . E 2 IR3 1 1380 1380 IR3 IR3 A . F 2 IR3 1 1379 1379 IR3 IR3 B . G 3 NAG 1 1380 1380 NAG NAG B . H 2 IR3 1 1381 1381 IR3 IR3 B . I 4 HOH 1 2001 2001 HOH HOH A . I 4 HOH 2 2002 2002 HOH HOH A . I 4 HOH 3 2003 2003 HOH HOH A . I 4 HOH 4 2004 2004 HOH HOH A . J 4 HOH 1 2001 2001 HOH HOH B . J 4 HOH 2 2002 2002 HOH HOH B . J 4 HOH 3 2003 2003 HOH HOH B . J 4 HOH 4 2004 2004 HOH HOH B . J 4 HOH 5 2005 2005 HOH HOH B . J 4 HOH 6 2006 2006 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ASN 70 A ASN 291 ? ASN 'GLYCOSYLATION SITE' 2 B ASN 70 B ASN 291 ? ASN 'GLYCOSYLATION SITE' # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,D,E,I 2 1 B,F,G,H,J # _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 2012-08-15 2 'Structure model' 1 1 2017-07-12 3 'Structure model' 1 2 2019-07-17 4 'Structure model' 1 3 2020-07-29 # 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' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Derived calculations' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 4 'Structure model' 'Structure summary' # 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 2 'Structure model' software 2 3 'Structure model' diffrn_source 3 3 'Structure model' struct_conn 4 4 'Structure model' chem_comp 5 4 'Structure model' entity 6 4 'Structure model' pdbx_chem_comp_identifier 7 4 'Structure model' pdbx_database_status 8 4 'Structure model' pdbx_entity_nonpoly 9 4 'Structure model' struct_conn 10 4 'Structure model' struct_site 11 4 'Structure model' struct_site_gen # 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 2 'Structure model' '_software.name' 2 3 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_chem_comp.name' 5 4 'Structure model' '_chem_comp.type' 6 4 'Structure model' '_entity.pdbx_description' 7 4 'Structure model' '_pdbx_database_status.status_code_sf' 8 4 'Structure model' '_pdbx_entity_nonpoly.name' 9 4 'Structure model' '_struct_conn.pdbx_role' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHENIX refinement '(PHENIX.REFINE)' ? 1 XDS 'data reduction' . ? 2 XSCALE 'data scaling' . ? 3 PHENIX phasing . ? 4 # _pdbx_entry_details.entry_id 4AKM _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ;N-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYL-D-GLUCOSAMINE IS COVALENTLY ATTACHED TO N291 ; _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 CB B CYS 237 ? ? SG B CYS 274 ? ? 1.87 2 1 CB A CYS 237 ? ? SG A CYS 274 ? ? 2.07 # 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 SER A 234 ? ? -145.37 -30.05 2 1 MET A 242 ? ? 178.13 164.11 3 1 GLU A 298 ? ? 64.72 110.10 4 1 SER A 300 ? ? 89.14 146.63 5 1 PRO A 315 ? ? -51.96 -70.01 6 1 GLU A 316 ? ? 170.36 59.80 7 1 CYS A 339 ? ? -163.55 90.32 8 1 SER A 348 ? ? -121.28 -163.13 9 1 PHE A 363 ? ? 68.36 -96.88 10 1 ASN A 372 ? ? -66.52 4.59 11 1 VAL A 373 ? ? 63.63 156.89 12 1 VAL B 223 ? ? 55.16 71.46 13 1 SER B 256 ? ? -163.93 69.91 14 1 GLN B 286 ? ? -58.48 98.84 15 1 GLU B 298 ? ? 67.02 131.23 16 1 GLU B 299 ? ? -92.03 36.25 17 1 ASP B 314 ? ? 53.39 77.08 18 1 CYS B 339 ? ? -160.67 98.42 19 1 PHE B 363 ? ? 83.84 -50.25 20 1 CYS B 376 ? ? -87.56 -104.88 21 1 SER B 377 ? ? -172.23 100.89 # 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 SER 222 ? A SER 1 2 1 Y 1 A SER 378 ? A SER 157 3 1 Y 1 A ASP 379 ? A ASP 158 4 1 Y 1 A TYR 380 ? A TYR 159 5 1 Y 1 A THR 381 ? A THR 160 6 1 Y 1 A HIS 382 ? A HIS 161 7 1 Y 1 A HIS 383 ? A HIS 162 8 1 Y 1 A HIS 384 ? A HIS 163 9 1 Y 1 A HIS 385 ? A HIS 164 10 1 Y 1 A HIS 386 ? A HIS 165 11 1 Y 1 A HIS 387 ? A HIS 166 12 1 Y 1 B ASP 379 ? B ASP 158 13 1 Y 1 B TYR 380 ? B TYR 159 14 1 Y 1 B THR 381 ? B THR 160 15 1 Y 1 B HIS 382 ? B HIS 161 16 1 Y 1 B HIS 383 ? B HIS 162 17 1 Y 1 B HIS 384 ? B HIS 163 18 1 Y 1 B HIS 385 ? B HIS 164 19 1 Y 1 B HIS 386 ? B HIS 165 20 1 Y 1 B HIS 387 ? B HIS 166 # 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 'IRIDIUM (III) ION' IR3 3 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 4 water HOH #