data_2VKI # _entry.id 2VKI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.382 _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 2VKI pdb_00002vki 10.2210/pdb2vki/pdb PDBE EBI-34836 ? ? WWPDB D_1290034836 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1UU8 unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1' PDB 1OKY unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE' PDB 1Z5M unspecified ;CRYSTAL STRUCTURE OF N1-[3-[[5-BROMO-2-[[ 3-[(1-PYRROLIDINYLCARBONYL)AMINO]PHENYL]AMINO ]-4-PYRIMIDINYL]AMINO]PROPYL]-2,2- DIMETHYLPROPANEDIAMIDECOMPLEXED WITH HUMAN PDK1 ; PDB 1UU9 unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3' PDB 1OKZ unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01' PDB 1W1D unspecified 'CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND TO INOSITOL (1, 3,4,5)-TETRAKISPHOSPHATE' PDB 1H1W unspecified 'HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 CATALYTIC DOMAIN' PDB 1UU3 unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531' PDB 1W1G unspecified 'CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND TO DIC4- PHOSPHATIDYLINOSITOL (3,4,5)-TRISPHOSPHATE' PDB 2BIY unspecified 'STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN' PDB 1W1H unspecified 'CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN' PDB 1UU7 unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-2' PDB 1UVR unspecified 'STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2VKI _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2007-12-19 _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 'Komander, D.' 1 'Bayascas, J.R.' 2 'Deak, M.' 3 'Alessi, D.R.' 4 'van Aalten, D.M.F.' 5 # _citation.id primary _citation.title 'Mutation of the Pdk1 Ph Domain Inhibits Protein Kinase B/Akt, Leading to Small Size and Insulin Resistance.' _citation.journal_abbrev Mol.Cell.Biol. _citation.journal_volume 28 _citation.page_first 3258 _citation.page_last ? _citation.year 2008 _citation.journal_id_ASTM MCEBD4 _citation.country US _citation.journal_id_ISSN 0270-7306 _citation.journal_id_CSD 2044 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18347057 _citation.pdbx_database_id_DOI 10.1128/MCB.02032-07 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bayascas, J.R.' 1 ? primary 'Wullschleger, S.' 2 ? primary 'Sakamoto, K.' 3 ? primary 'Garcia-Martinez, J.M.' 4 ? primary 'Clacher, C.' 5 ? primary 'Komander, D.' 6 ? primary 'Van Aalten, D.M.F.' 7 ? primary 'Boini, K.M.' 8 ? primary 'Lang, F.' 9 ? primary 'Lipina, C.' 10 ? primary 'Logie, L.' 11 ? primary 'Sutherland, C.' 12 ? primary 'Chudek, J.A.' 13 ? primary 'Van Diepen, J.A.' 14 ? primary 'Voshol, P.J.' 15 ? primary 'Lucocq, J.M.' 16 ? primary 'Alessi, D.R.' 17 ? # _cell.entry_id 2VKI _cell.length_a 34.009 _cell.length_b 67.057 _cell.length_c 67.802 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VKI _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # 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 '3-PHOPSHOINOSITIDE DEPENDENT PROTEIN KINASE 1' 17548.791 1 2.7.11.1 YES 'PLECKSTRIN HOMOLOGY (PH) DOMAIN, RESIDUES 409-556' ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 water nat water 18.015 112 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name HPDK1 # _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 ;GSNIEQYIHDLDSNSFELDLQFSEDEKRLLLEKQAGGNPWHQFVENNLILKMGPVDERKGLFARRRQLLLTEGPHLYYVD PVNKVLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ ; _entity_poly.pdbx_seq_one_letter_code_can ;GSNIEQYIHDLDSNSFELDLQFSEDEKRLLLEKQAGGNPWHQFVENNLILKMGPVDERKGLFARRRQLLLTEGPHLYYVD PVNKVLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ ; _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 SER n 1 3 ASN n 1 4 ILE n 1 5 GLU n 1 6 GLN n 1 7 TYR n 1 8 ILE n 1 9 HIS n 1 10 ASP n 1 11 LEU n 1 12 ASP n 1 13 SER n 1 14 ASN n 1 15 SER n 1 16 PHE n 1 17 GLU n 1 18 LEU n 1 19 ASP n 1 20 LEU n 1 21 GLN n 1 22 PHE n 1 23 SER n 1 24 GLU n 1 25 ASP n 1 26 GLU n 1 27 LYS n 1 28 ARG n 1 29 LEU n 1 30 LEU n 1 31 LEU n 1 32 GLU n 1 33 LYS n 1 34 GLN n 1 35 ALA n 1 36 GLY n 1 37 GLY n 1 38 ASN n 1 39 PRO n 1 40 TRP n 1 41 HIS n 1 42 GLN n 1 43 PHE n 1 44 VAL n 1 45 GLU n 1 46 ASN n 1 47 ASN n 1 48 LEU n 1 49 ILE n 1 50 LEU n 1 51 LYS n 1 52 MET n 1 53 GLY n 1 54 PRO n 1 55 VAL n 1 56 ASP n 1 57 GLU n 1 58 ARG n 1 59 LYS n 1 60 GLY n 1 61 LEU n 1 62 PHE n 1 63 ALA n 1 64 ARG n 1 65 ARG n 1 66 ARG n 1 67 GLN n 1 68 LEU n 1 69 LEU n 1 70 LEU n 1 71 THR n 1 72 GLU n 1 73 GLY n 1 74 PRO n 1 75 HIS n 1 76 LEU n 1 77 TYR n 1 78 TYR n 1 79 VAL n 1 80 ASP n 1 81 PRO n 1 82 VAL n 1 83 ASN n 1 84 LYS n 1 85 VAL n 1 86 LEU n 1 87 LYS n 1 88 GLY n 1 89 GLU n 1 90 ILE n 1 91 PRO n 1 92 TRP n 1 93 SER n 1 94 GLN n 1 95 GLU n 1 96 LEU n 1 97 ARG n 1 98 PRO n 1 99 GLU n 1 100 ALA n 1 101 LYS n 1 102 ASN n 1 103 PHE n 1 104 LYS n 1 105 THR n 1 106 PHE n 1 107 PHE n 1 108 VAL n 1 109 HIS n 1 110 THR n 1 111 PRO n 1 112 ASN n 1 113 ARG n 1 114 THR n 1 115 TYR n 1 116 TYR n 1 117 LEU n 1 118 MET n 1 119 ASP n 1 120 PRO n 1 121 SER n 1 122 GLY n 1 123 ASN n 1 124 ALA n 1 125 HIS n 1 126 LYS n 1 127 TRP n 1 128 CYS n 1 129 ARG n 1 130 LYS n 1 131 ILE n 1 132 GLN n 1 133 GLU n 1 134 VAL n 1 135 TRP n 1 136 ARG n 1 137 GLN n 1 138 ARG n 1 139 TYR n 1 140 GLN n 1 141 SER n 1 142 HIS n 1 143 PRO n 1 144 ASP n 1 145 ALA n 1 146 ALA n 1 147 VAL n 1 148 GLN 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 ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'BL21(DE3)' _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 ? _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 PGEX6P1 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PDPK1_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession O15530 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2VKI _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 148 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O15530 _struct_ref_seq.db_align_beg 409 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 556 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 409 _struct_ref_seq.pdbx_auth_seq_align_end 556 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2VKI _struct_ref_seq_dif.mon_id GLU _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 57 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code O15530 _struct_ref_seq_dif.db_mon_id LYS _struct_ref_seq_dif.pdbx_seq_db_seq_num 465 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 465 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 2VKI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.2 _exptl_crystal.density_percent_sol 44 _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 8.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '0.2 M LITHIUM SULPHATE, 0.1 M TRIS HYDROCHLORIDE [PH 8.5] 30 % (W/V) PEG 4000' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU IMAGE PLATE' _diffrn_detector.pdbx_collection_date 2004-06-30 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-007' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2VKI _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25.00 _reflns.d_resolution_high 1.80 _reflns.number_obs 14950 _reflns.number_all ? _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 10.00 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.5 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.86 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.55 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.30 _reflns_shell.pdbx_redundancy 4.3 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2VKI _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.ls_number_reflns_obs 14309 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 25.00 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 99.5 _refine.ls_R_factor_obs 0.175 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.173 _refine.ls_R_factor_R_free 0.215 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.100 _refine.ls_number_reflns_R_free 609 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.966 _refine.correlation_coeff_Fo_to_Fc_free 0.952 _refine.B_iso_mean 21.05 _refine.aniso_B[1][1] 0.12000 _refine.aniso_B[2][2] -0.64000 _refine.aniso_B[3][3] 0.52000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES WERE MODELLED AS ALA OR WITH OCCU 0.01. THE C-TERMINUS IS DISORDERED. ; _refine.pdbx_starting_model 'PDB ENTRY 1W1D' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.121 _refine.pdbx_overall_ESU_R_Free 0.120 _refine.overall_SU_ML 0.084 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.765 _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 1172 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 112 _refine_hist.number_atoms_total 1295 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 25.00 # 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 r_bond_refined_d 0.016 0.021 ? 1242 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 1101 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.681 1.944 ? 1677 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.904 3.000 ? 2566 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.298 5.000 ? 138 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.106 0.200 ? 170 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.020 ? 1354 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.011 0.020 ? 271 'X-RAY DIFFRACTION' ? r_nbd_refined 0.216 0.200 ? 215 'X-RAY DIFFRACTION' ? r_nbd_other 0.253 0.200 ? 1257 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other 0.086 0.200 ? 730 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.160 0.200 ? 89 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.190 0.200 ? 17 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.312 0.200 ? 79 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.117 0.200 ? 12 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.983 1.500 ? 700 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.780 2.000 ? 1137 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.542 3.000 ? 542 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 4.059 4.500 ? 540 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.80 _refine_ls_shell.d_res_low 1.84 _refine_ls_shell.number_reflns_R_work 1000 _refine_ls_shell.R_factor_R_work 0.2680 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.3480 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 45 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2VKI _struct.title 'Structure of the PDK1 PH domain K465E mutant' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2VKI _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text 'PLECKSTRIN HOMOLOGY, TRANSFERASE, CANCER, DIABETES' # 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 ? # _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 ASN A 3 ? GLN A 6 ? ASN A 411 GLN A 414 5 ? 4 HELX_P HELX_P2 2 SER A 23 ? ASN A 38 ? SER A 431 ASN A 446 1 ? 16 HELX_P HELX_P3 3 TRP A 40 ? VAL A 44 ? TRP A 448 VAL A 452 5 ? 5 HELX_P HELX_P4 4 ASN A 123 ? GLN A 140 ? ASN A 531 GLN A 548 1 ? 18 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLY _struct_mon_prot_cis.label_seq_id 73 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLY _struct_mon_prot_cis.auth_seq_id 481 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 74 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 482 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -4.30 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 6 ? AB ? 6 ? # 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 AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AA 4 5 ? anti-parallel AA 5 6 ? anti-parallel AB 1 2 ? anti-parallel AB 2 3 ? anti-parallel AB 3 4 ? anti-parallel AB 4 5 ? anti-parallel AB 5 6 ? 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 ILE A 8 ? ASP A 12 ? ILE A 416 ASP A 420 AA 2 SER A 15 ? LEU A 18 ? SER A 423 LEU A 426 AA 3 ILE A 49 ? GLU A 57 ? ILE A 457 GLU A 465 AA 4 ARG A 64 ? THR A 71 ? ARG A 472 THR A 479 AA 5 HIS A 75 ? ASP A 80 ? HIS A 483 ASP A 488 AA 6 VAL A 85 ? ILE A 90 ? VAL A 493 ILE A 498 AB 1 ILE A 8 ? ASP A 12 ? ILE A 416 ASP A 420 AB 2 SER A 15 ? LEU A 18 ? SER A 423 LEU A 426 AB 3 ILE A 49 ? GLU A 57 ? ILE A 457 GLU A 465 AB 4 ARG A 113 ? MET A 118 ? ARG A 521 MET A 526 AB 5 THR A 105 ? THR A 110 ? THR A 513 THR A 518 AB 6 ARG A 97 ? ALA A 100 ? ARG A 505 ALA A 508 # 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 LEU A 11 ? N LEU A 419 O SER A 15 ? O SER A 423 AA 2 3 N LEU A 18 ? N LEU A 426 O LEU A 50 ? O LEU A 458 AA 3 4 N GLU A 57 ? N GLU A 465 O ARG A 64 ? O ARG A 472 AA 4 5 N THR A 71 ? N THR A 479 O HIS A 75 ? O HIS A 483 AA 5 6 N ASP A 80 ? N ASP A 488 O VAL A 85 ? O VAL A 493 AB 1 2 N LEU A 11 ? N LEU A 419 O SER A 15 ? O SER A 423 AB 2 3 N LEU A 18 ? N LEU A 426 O LEU A 50 ? O LEU A 458 AB 3 4 N ASP A 56 ? N ASP A 464 O MET A 118 ? O MET A 526 AB 4 5 N LEU A 117 ? N LEU A 525 O PHE A 106 ? O PHE A 514 AB 5 6 N HIS A 109 ? N HIS A 517 O ARG A 97 ? O ARG A 505 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE GOL A1549' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE SO4 A1550' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 SER A 23 ? SER A 431 . ? 1_555 ? 2 AC1 4 GLU A 24 ? GLU A 432 . ? 1_555 ? 3 AC1 4 ASP A 25 ? ASP A 433 . ? 1_555 ? 4 AC1 4 ARG A 113 ? ARG A 521 . ? 1_555 ? 5 AC2 3 LYS A 59 ? LYS A 467 . ? 1_555 ? 6 AC2 3 ARG A 64 ? ARG A 472 . ? 1_555 ? 7 AC2 3 ARG A 66 ? ARG A 474 . ? 1_555 ? # _database_PDB_matrix.entry_id 2VKI _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 2VKI _atom_sites.fract_transf_matrix[1][1] 0.029404 _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] 0.014913 _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] 0.014749 _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 1 409 ? ? ? A . n A 1 2 SER 2 410 410 SER SER A . n A 1 3 ASN 3 411 411 ASN ASN A . n A 1 4 ILE 4 412 412 ILE ILE A . n A 1 5 GLU 5 413 413 GLU GLU A . n A 1 6 GLN 6 414 414 GLN GLN A . n A 1 7 TYR 7 415 415 TYR TYR A . n A 1 8 ILE 8 416 416 ILE ILE A . n A 1 9 HIS 9 417 417 HIS HIS A . n A 1 10 ASP 10 418 418 ASP ASP A . n A 1 11 LEU 11 419 419 LEU LEU A . n A 1 12 ASP 12 420 420 ASP ASP A . n A 1 13 SER 13 421 421 SER SER A . n A 1 14 ASN 14 422 422 ASN ASN A . n A 1 15 SER 15 423 423 SER SER A . n A 1 16 PHE 16 424 424 PHE PHE A . n A 1 17 GLU 17 425 425 GLU GLU A . n A 1 18 LEU 18 426 426 LEU LEU A . n A 1 19 ASP 19 427 427 ASP ASP A . n A 1 20 LEU 20 428 428 LEU LEU A . n A 1 21 GLN 21 429 429 GLN GLN A . n A 1 22 PHE 22 430 430 PHE PHE A . n A 1 23 SER 23 431 431 SER SER A . n A 1 24 GLU 24 432 432 GLU GLU A . n A 1 25 ASP 25 433 433 ASP ASP A . n A 1 26 GLU 26 434 434 GLU GLU A . n A 1 27 LYS 27 435 435 LYS LYS A . n A 1 28 ARG 28 436 436 ARG ARG A . n A 1 29 LEU 29 437 437 LEU LEU A . n A 1 30 LEU 30 438 438 LEU LEU A . n A 1 31 LEU 31 439 439 LEU LEU A . n A 1 32 GLU 32 440 440 GLU GLU A . n A 1 33 LYS 33 441 441 LYS LYS A . n A 1 34 GLN 34 442 442 GLN GLN A . n A 1 35 ALA 35 443 443 ALA ALA A . n A 1 36 GLY 36 444 444 GLY GLY A . n A 1 37 GLY 37 445 445 GLY GLY A . n A 1 38 ASN 38 446 446 ASN ASN A . n A 1 39 PRO 39 447 447 PRO PRO A . n A 1 40 TRP 40 448 448 TRP TRP A . n A 1 41 HIS 41 449 449 HIS HIS A . n A 1 42 GLN 42 450 450 GLN GLN A . n A 1 43 PHE 43 451 451 PHE PHE A . n A 1 44 VAL 44 452 452 VAL VAL A . n A 1 45 GLU 45 453 453 GLU GLU A . n A 1 46 ASN 46 454 454 ASN ASN A . n A 1 47 ASN 47 455 455 ASN ASN A . n A 1 48 LEU 48 456 456 LEU LEU A . n A 1 49 ILE 49 457 457 ILE ILE A . n A 1 50 LEU 50 458 458 LEU LEU A . n A 1 51 LYS 51 459 459 LYS LYS A . n A 1 52 MET 52 460 460 MET MET A . n A 1 53 GLY 53 461 461 GLY GLY A . n A 1 54 PRO 54 462 462 PRO PRO A . n A 1 55 VAL 55 463 463 VAL VAL A . n A 1 56 ASP 56 464 464 ASP ASP A . n A 1 57 GLU 57 465 465 GLU GLU A . n A 1 58 ARG 58 466 466 ARG ARG A . n A 1 59 LYS 59 467 467 LYS LYS A . n A 1 60 GLY 60 468 468 GLY GLY A . n A 1 61 LEU 61 469 469 LEU LEU A . n A 1 62 PHE 62 470 470 PHE PHE A . n A 1 63 ALA 63 471 471 ALA ALA A . n A 1 64 ARG 64 472 472 ARG ARG A . n A 1 65 ARG 65 473 473 ARG ARG A . n A 1 66 ARG 66 474 474 ARG ARG A . n A 1 67 GLN 67 475 475 GLN GLN A . n A 1 68 LEU 68 476 476 LEU LEU A . n A 1 69 LEU 69 477 477 LEU LEU A . n A 1 70 LEU 70 478 478 LEU LEU A . n A 1 71 THR 71 479 479 THR THR A . n A 1 72 GLU 72 480 480 GLU GLU A . n A 1 73 GLY 73 481 481 GLY GLY A . n A 1 74 PRO 74 482 482 PRO PRO A . n A 1 75 HIS 75 483 483 HIS HIS A . n A 1 76 LEU 76 484 484 LEU LEU A . n A 1 77 TYR 77 485 485 TYR TYR A . n A 1 78 TYR 78 486 486 TYR TYR A . n A 1 79 VAL 79 487 487 VAL VAL A . n A 1 80 ASP 80 488 488 ASP ASP A . n A 1 81 PRO 81 489 489 PRO PRO A . n A 1 82 VAL 82 490 490 VAL VAL A . n A 1 83 ASN 83 491 491 ASN ASN A . n A 1 84 LYS 84 492 492 LYS LYS A . n A 1 85 VAL 85 493 493 VAL VAL A . n A 1 86 LEU 86 494 494 LEU LEU A . n A 1 87 LYS 87 495 495 LYS LYS A . n A 1 88 GLY 88 496 496 GLY GLY A . n A 1 89 GLU 89 497 497 GLU GLU A . n A 1 90 ILE 90 498 498 ILE ILE A . n A 1 91 PRO 91 499 499 PRO PRO A . n A 1 92 TRP 92 500 500 TRP TRP A . n A 1 93 SER 93 501 501 SER SER A . n A 1 94 GLN 94 502 502 GLN GLN A . n A 1 95 GLU 95 503 503 GLU GLU A . n A 1 96 LEU 96 504 504 LEU LEU A . n A 1 97 ARG 97 505 505 ARG ARG A . n A 1 98 PRO 98 506 506 PRO PRO A . n A 1 99 GLU 99 507 507 GLU GLU A . n A 1 100 ALA 100 508 508 ALA ALA A . n A 1 101 LYS 101 509 509 LYS LYS A . n A 1 102 ASN 102 510 510 ASN ASN A . n A 1 103 PHE 103 511 511 PHE PHE A . n A 1 104 LYS 104 512 512 LYS LYS A . n A 1 105 THR 105 513 513 THR THR A . n A 1 106 PHE 106 514 514 PHE PHE A . n A 1 107 PHE 107 515 515 PHE PHE A . n A 1 108 VAL 108 516 516 VAL VAL A . n A 1 109 HIS 109 517 517 HIS HIS A . n A 1 110 THR 110 518 518 THR THR A . n A 1 111 PRO 111 519 519 PRO PRO A . n A 1 112 ASN 112 520 520 ASN ASN A . n A 1 113 ARG 113 521 521 ARG ARG A . n A 1 114 THR 114 522 522 THR THR A . n A 1 115 TYR 115 523 523 TYR TYR A . n A 1 116 TYR 116 524 524 TYR TYR A . n A 1 117 LEU 117 525 525 LEU LEU A . n A 1 118 MET 118 526 526 MET MET A . n A 1 119 ASP 119 527 527 ASP ASP A . n A 1 120 PRO 120 528 528 PRO PRO A . n A 1 121 SER 121 529 529 SER SER A . n A 1 122 GLY 122 530 530 GLY GLY A . n A 1 123 ASN 123 531 531 ASN ASN A . n A 1 124 ALA 124 532 532 ALA ALA A . n A 1 125 HIS 125 533 533 HIS HIS A . n A 1 126 LYS 126 534 534 LYS LYS A . n A 1 127 TRP 127 535 535 TRP TRP A . n A 1 128 CYS 128 536 536 CYS CYS A . n A 1 129 ARG 129 537 537 ARG ARG A . n A 1 130 LYS 130 538 538 LYS LYS A . n A 1 131 ILE 131 539 539 ILE ILE A . n A 1 132 GLN 132 540 540 GLN GLN A . n A 1 133 GLU 133 541 541 GLU GLU A . n A 1 134 VAL 134 542 542 VAL VAL A . n A 1 135 TRP 135 543 543 TRP TRP A . n A 1 136 ARG 136 544 544 ARG ARG A . n A 1 137 GLN 137 545 545 GLN GLN A . n A 1 138 ARG 138 546 546 ARG ARG A . n A 1 139 TYR 139 547 547 TYR TYR A . n A 1 140 GLN 140 548 548 GLN GLN A . n A 1 141 SER 141 549 549 SER SER A . n A 1 142 HIS 142 550 ? ? ? A . n A 1 143 PRO 143 551 ? ? ? A . n A 1 144 ASP 144 552 ? ? ? A . n A 1 145 ALA 145 553 ? ? ? A . n A 1 146 ALA 146 554 ? ? ? A . n A 1 147 VAL 147 555 ? ? ? A . n A 1 148 GLN 148 556 ? ? ? 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 GOL 1 1549 1549 GOL GOL A . C 3 SO4 1 1550 1550 SO4 SO4 A . D 4 HOH 1 2001 2001 HOH HOH A . D 4 HOH 2 2002 2002 HOH HOH A . D 4 HOH 3 2003 2003 HOH HOH A . D 4 HOH 4 2004 2004 HOH HOH A . D 4 HOH 5 2005 2005 HOH HOH A . D 4 HOH 6 2006 2006 HOH HOH A . D 4 HOH 7 2007 2007 HOH HOH A . D 4 HOH 8 2008 2008 HOH HOH A . D 4 HOH 9 2009 2009 HOH HOH A . D 4 HOH 10 2010 2010 HOH HOH A . D 4 HOH 11 2011 2011 HOH HOH A . D 4 HOH 12 2012 2012 HOH HOH A . D 4 HOH 13 2013 2013 HOH HOH A . D 4 HOH 14 2014 2014 HOH HOH A . D 4 HOH 15 2015 2015 HOH HOH A . D 4 HOH 16 2016 2016 HOH HOH A . D 4 HOH 17 2017 2017 HOH HOH A . D 4 HOH 18 2018 2018 HOH HOH A . D 4 HOH 19 2019 2019 HOH HOH A . D 4 HOH 20 2020 2020 HOH HOH A . D 4 HOH 21 2021 2021 HOH HOH A . D 4 HOH 22 2022 2022 HOH HOH A . D 4 HOH 23 2023 2023 HOH HOH A . D 4 HOH 24 2024 2024 HOH HOH A . D 4 HOH 25 2025 2025 HOH HOH A . D 4 HOH 26 2026 2026 HOH HOH A . D 4 HOH 27 2027 2027 HOH HOH A . D 4 HOH 28 2028 2028 HOH HOH A . D 4 HOH 29 2029 2029 HOH HOH A . D 4 HOH 30 2030 2030 HOH HOH A . D 4 HOH 31 2031 2031 HOH HOH A . D 4 HOH 32 2032 2032 HOH HOH A . D 4 HOH 33 2033 2033 HOH HOH A . D 4 HOH 34 2034 2034 HOH HOH A . D 4 HOH 35 2035 2035 HOH HOH A . D 4 HOH 36 2036 2036 HOH HOH A . D 4 HOH 37 2037 2037 HOH HOH A . D 4 HOH 38 2038 2038 HOH HOH A . D 4 HOH 39 2039 2039 HOH HOH A . D 4 HOH 40 2040 2040 HOH HOH A . D 4 HOH 41 2041 2041 HOH HOH A . D 4 HOH 42 2042 2042 HOH HOH A . D 4 HOH 43 2043 2043 HOH HOH A . D 4 HOH 44 2044 2044 HOH HOH A . D 4 HOH 45 2045 2045 HOH HOH A . D 4 HOH 46 2046 2046 HOH HOH A . D 4 HOH 47 2047 2047 HOH HOH A . D 4 HOH 48 2048 2048 HOH HOH A . D 4 HOH 49 2049 2049 HOH HOH A . D 4 HOH 50 2050 2050 HOH HOH A . D 4 HOH 51 2051 2051 HOH HOH A . D 4 HOH 52 2052 2052 HOH HOH A . D 4 HOH 53 2053 2053 HOH HOH A . D 4 HOH 54 2054 2054 HOH HOH A . D 4 HOH 55 2055 2055 HOH HOH A . D 4 HOH 56 2056 2056 HOH HOH A . D 4 HOH 57 2057 2057 HOH HOH A . D 4 HOH 58 2058 2058 HOH HOH A . D 4 HOH 59 2059 2059 HOH HOH A . D 4 HOH 60 2060 2060 HOH HOH A . D 4 HOH 61 2061 2061 HOH HOH A . D 4 HOH 62 2062 2062 HOH HOH A . D 4 HOH 63 2063 2063 HOH HOH A . D 4 HOH 64 2064 2064 HOH HOH A . D 4 HOH 65 2065 2065 HOH HOH A . D 4 HOH 66 2066 2066 HOH HOH A . D 4 HOH 67 2067 2067 HOH HOH A . D 4 HOH 68 2068 2068 HOH HOH A . D 4 HOH 69 2069 2069 HOH HOH A . D 4 HOH 70 2070 2070 HOH HOH A . D 4 HOH 71 2071 2071 HOH HOH A . D 4 HOH 72 2072 2072 HOH HOH A . D 4 HOH 73 2073 2073 HOH HOH A . D 4 HOH 74 2074 2074 HOH HOH A . D 4 HOH 75 2075 2075 HOH HOH A . D 4 HOH 76 2076 2076 HOH HOH A . D 4 HOH 77 2077 2077 HOH HOH A . D 4 HOH 78 2078 2078 HOH HOH A . D 4 HOH 79 2079 2079 HOH HOH A . D 4 HOH 80 2080 2080 HOH HOH A . D 4 HOH 81 2081 2081 HOH HOH A . D 4 HOH 82 2082 2082 HOH HOH A . D 4 HOH 83 2083 2083 HOH HOH A . D 4 HOH 84 2084 2084 HOH HOH A . D 4 HOH 85 2085 2085 HOH HOH A . D 4 HOH 86 2086 2086 HOH HOH A . D 4 HOH 87 2087 2087 HOH HOH A . D 4 HOH 88 2088 2088 HOH HOH A . D 4 HOH 89 2089 2089 HOH HOH A . D 4 HOH 90 2090 2090 HOH HOH A . D 4 HOH 91 2091 2091 HOH HOH A . D 4 HOH 92 2092 2092 HOH HOH A . D 4 HOH 93 2093 2093 HOH HOH A . D 4 HOH 94 2094 2094 HOH HOH A . D 4 HOH 95 2095 2095 HOH HOH A . D 4 HOH 96 2096 2096 HOH HOH A . D 4 HOH 97 2097 2097 HOH HOH A . D 4 HOH 98 2098 2098 HOH HOH A . D 4 HOH 99 2099 2099 HOH HOH A . D 4 HOH 100 2100 2100 HOH HOH A . D 4 HOH 101 2101 2101 HOH HOH A . D 4 HOH 102 2102 2102 HOH HOH A . D 4 HOH 103 2103 2103 HOH HOH A . D 4 HOH 104 2104 2104 HOH HOH A . D 4 HOH 105 2105 2105 HOH HOH A . D 4 HOH 106 2106 2106 HOH HOH A . D 4 HOH 107 2107 2107 HOH HOH A . D 4 HOH 108 2108 2108 HOH HOH A . D 4 HOH 109 2109 2109 HOH HOH A . D 4 HOH 110 2110 2110 HOH HOH A . D 4 HOH 111 2111 2111 HOH HOH A . D 4 HOH 112 2112 2112 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # _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 2008-05-13 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-12-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # 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' Advisory 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' Other 7 3 'Structure model' 'Refinement description' # 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_database_status 5 3 'Structure model' pdbx_initial_refinement_model # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_sf' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 1.9703 17.6963 11.1860 0.0395 0.0345 0.0428 -0.0056 -0.0072 -0.0087 0.3314 1.1483 0.8004 -0.1515 0.1228 -0.1352 -0.0030 -0.0485 -0.0011 0.0306 0.0445 -0.0373 -0.0251 0.0218 -0.0415 'X-RAY DIFFRACTION' 2 ? refined -0.7469 16.3049 12.3078 0.0117 0.0128 0.0388 0.0080 -0.0076 -0.0209 0.5356 0.2234 1.0095 -0.2601 0.1261 -0.0010 -0.0394 -0.0679 0.0286 0.0022 0.0407 0.0228 0.0028 -0.0211 -0.0013 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 414 ? ? A 466 ? ? ? ? 'X-RAY DIFFRACTION' 2 1 A 472 ? ? A 487 ? ? ? ? 'X-RAY DIFFRACTION' 3 1 A 494 ? ? A 543 ? ? ? ? 'X-RAY DIFFRACTION' 4 2 A 410 ? ? A 413 ? ? ? ? 'X-RAY DIFFRACTION' 5 2 A 467 ? ? A 471 ? ? ? ? 'X-RAY DIFFRACTION' 6 2 A 544 ? ? A 549 ? ? ? ? 'X-RAY DIFFRACTION' 7 2 A 488 ? ? A 493 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 AMoRE phasing . ? 4 # _pdbx_database_remark.id 700 _pdbx_database_remark.text ; SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. ; # _pdbx_entry_details.entry_id 2VKI _pdbx_entry_details.compound_details 'ENGINEERED RESIDUE IN CHAIN A, LYS 465 TO GLU' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'POINT MUTATION K465E' _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A ASP 464 ? ? CG A ASP 464 ? ? OD1 A ASP 464 ? ? 123.72 118.30 5.42 0.90 N 2 1 NE A ARG 472 ? ? CZ A ARG 472 ? ? NH2 A ARG 472 ? ? 116.70 120.30 -3.60 0.50 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 GLN A 429 ? ? -99.73 52.95 2 1 GLU A 480 ? ? -39.20 143.53 3 1 GLN A 548 ? ? 121.69 -70.98 # 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 GLN 429 ? CG ? A GLN 21 CG 2 1 Y 1 A GLN 429 ? CD ? A GLN 21 CD 3 1 Y 1 A GLN 429 ? OE1 ? A GLN 21 OE1 4 1 Y 1 A GLN 429 ? NE2 ? A GLN 21 NE2 5 1 Y 1 A GLN 548 ? CG ? A GLN 140 CG 6 1 Y 1 A GLN 548 ? CD ? A GLN 140 CD 7 1 Y 1 A GLN 548 ? OE1 ? A GLN 140 OE1 8 1 Y 1 A GLN 548 ? NE2 ? A GLN 140 NE2 9 1 Y 1 A SER 549 ? CA ? A SER 141 CA 10 1 Y 1 A SER 549 ? C ? A SER 141 C 11 1 Y 1 A SER 549 ? O ? A SER 141 O 12 1 Y 1 A SER 549 ? CB ? A SER 141 CB 13 1 Y 1 A SER 549 ? OG ? A SER 141 OG # 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 409 ? A GLY 1 2 1 Y 1 A HIS 550 ? A HIS 142 3 1 Y 1 A PRO 551 ? A PRO 143 4 1 Y 1 A ASP 552 ? A ASP 144 5 1 Y 1 A ALA 553 ? A ALA 145 6 1 Y 1 A ALA 554 ? A ALA 146 7 1 Y 1 A VAL 555 ? A VAL 147 8 1 Y 1 A GLN 556 ? A GLN 148 # 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 GOL C1 C N N 137 GOL O1 O N N 138 GOL C2 C N N 139 GOL O2 O N N 140 GOL C3 C N N 141 GOL O3 O N N 142 GOL H11 H N N 143 GOL H12 H N N 144 GOL HO1 H N N 145 GOL H2 H N N 146 GOL HO2 H N N 147 GOL H31 H N N 148 GOL H32 H N N 149 GOL HO3 H N N 150 HIS N N N N 151 HIS CA C N S 152 HIS C C N N 153 HIS O O N N 154 HIS CB C N N 155 HIS CG C Y N 156 HIS ND1 N Y N 157 HIS CD2 C Y N 158 HIS CE1 C Y N 159 HIS NE2 N Y N 160 HIS OXT O N N 161 HIS H H N N 162 HIS H2 H N N 163 HIS HA H N N 164 HIS HB2 H N N 165 HIS HB3 H N N 166 HIS HD1 H N N 167 HIS HD2 H N N 168 HIS HE1 H N N 169 HIS HE2 H N N 170 HIS HXT H N N 171 HOH O O N N 172 HOH H1 H N N 173 HOH H2 H N N 174 ILE N N N N 175 ILE CA C N S 176 ILE C C N N 177 ILE O O N N 178 ILE CB C N S 179 ILE CG1 C N N 180 ILE CG2 C N N 181 ILE CD1 C N N 182 ILE OXT O N N 183 ILE H H N N 184 ILE H2 H N N 185 ILE HA H N N 186 ILE HB H N N 187 ILE HG12 H N N 188 ILE HG13 H N N 189 ILE HG21 H N N 190 ILE HG22 H N N 191 ILE HG23 H N N 192 ILE HD11 H N N 193 ILE HD12 H N N 194 ILE HD13 H N N 195 ILE HXT H N N 196 LEU N N N N 197 LEU CA C N S 198 LEU C C N N 199 LEU O O N N 200 LEU CB C N N 201 LEU CG C N N 202 LEU CD1 C N N 203 LEU CD2 C N N 204 LEU OXT O N N 205 LEU H H N N 206 LEU H2 H N N 207 LEU HA H N N 208 LEU HB2 H N N 209 LEU HB3 H N N 210 LEU HG H N N 211 LEU HD11 H N N 212 LEU HD12 H N N 213 LEU HD13 H N N 214 LEU HD21 H N N 215 LEU HD22 H N N 216 LEU HD23 H N N 217 LEU HXT H N N 218 LYS N N N N 219 LYS CA C N S 220 LYS C C N N 221 LYS O O N N 222 LYS CB C N N 223 LYS CG C N N 224 LYS CD C N N 225 LYS CE C N N 226 LYS NZ N N N 227 LYS OXT O N N 228 LYS H H N N 229 LYS H2 H N N 230 LYS HA H N N 231 LYS HB2 H N N 232 LYS HB3 H N N 233 LYS HG2 H N N 234 LYS HG3 H N N 235 LYS HD2 H N N 236 LYS HD3 H N N 237 LYS HE2 H N N 238 LYS HE3 H N N 239 LYS HZ1 H N N 240 LYS HZ2 H N N 241 LYS HZ3 H N N 242 LYS HXT H N N 243 MET N N N N 244 MET CA C N S 245 MET C C N N 246 MET O O N N 247 MET CB C N N 248 MET CG C N N 249 MET SD S N N 250 MET CE C N N 251 MET OXT O N N 252 MET H H N N 253 MET H2 H N N 254 MET HA H N N 255 MET HB2 H N N 256 MET HB3 H N N 257 MET HG2 H N N 258 MET HG3 H N N 259 MET HE1 H N N 260 MET HE2 H N N 261 MET HE3 H N N 262 MET HXT H N N 263 PHE N N N N 264 PHE CA C N S 265 PHE C C N N 266 PHE O O N N 267 PHE CB C N N 268 PHE CG C Y N 269 PHE CD1 C Y N 270 PHE CD2 C Y N 271 PHE CE1 C Y N 272 PHE CE2 C Y N 273 PHE CZ C Y N 274 PHE OXT O N N 275 PHE H H N N 276 PHE H2 H N N 277 PHE HA H N N 278 PHE HB2 H N N 279 PHE HB3 H N N 280 PHE HD1 H N N 281 PHE HD2 H N N 282 PHE HE1 H N N 283 PHE HE2 H N N 284 PHE HZ H N N 285 PHE HXT H N N 286 PRO N N N N 287 PRO CA C N S 288 PRO C C N N 289 PRO O O N N 290 PRO CB C N N 291 PRO CG C N N 292 PRO CD C N N 293 PRO OXT O N N 294 PRO H H N N 295 PRO HA H N N 296 PRO HB2 H N N 297 PRO HB3 H N N 298 PRO HG2 H N N 299 PRO HG3 H N N 300 PRO HD2 H N N 301 PRO HD3 H N N 302 PRO HXT H N N 303 SER N N N N 304 SER CA C N S 305 SER C C N N 306 SER O O N N 307 SER CB C N N 308 SER OG O N N 309 SER OXT O N N 310 SER H H N N 311 SER H2 H N N 312 SER HA H N N 313 SER HB2 H N N 314 SER HB3 H N N 315 SER HG H N N 316 SER HXT H N N 317 SO4 S S N N 318 SO4 O1 O N N 319 SO4 O2 O N N 320 SO4 O3 O N N 321 SO4 O4 O N N 322 THR N N N N 323 THR CA C N S 324 THR C C N N 325 THR O O N N 326 THR CB C N R 327 THR OG1 O N N 328 THR CG2 C N N 329 THR OXT O N N 330 THR H H N N 331 THR H2 H N N 332 THR HA H N N 333 THR HB H N N 334 THR HG1 H N N 335 THR HG21 H N N 336 THR HG22 H N N 337 THR HG23 H N N 338 THR HXT H N N 339 TRP N N N N 340 TRP CA C N S 341 TRP C C N N 342 TRP O O N N 343 TRP CB C N N 344 TRP CG C Y N 345 TRP CD1 C Y N 346 TRP CD2 C Y N 347 TRP NE1 N Y N 348 TRP CE2 C Y N 349 TRP CE3 C Y N 350 TRP CZ2 C Y N 351 TRP CZ3 C Y N 352 TRP CH2 C Y N 353 TRP OXT O N N 354 TRP H H N N 355 TRP H2 H N N 356 TRP HA H N N 357 TRP HB2 H N N 358 TRP HB3 H N N 359 TRP HD1 H N N 360 TRP HE1 H N N 361 TRP HE3 H N N 362 TRP HZ2 H N N 363 TRP HZ3 H N N 364 TRP HH2 H N N 365 TRP HXT H N N 366 TYR N N N N 367 TYR CA C N S 368 TYR C C N N 369 TYR O O N N 370 TYR CB C N N 371 TYR CG C Y N 372 TYR CD1 C Y N 373 TYR CD2 C Y N 374 TYR CE1 C Y N 375 TYR CE2 C Y N 376 TYR CZ C Y N 377 TYR OH O N N 378 TYR OXT O N N 379 TYR H H N N 380 TYR H2 H N N 381 TYR HA H N N 382 TYR HB2 H N N 383 TYR HB3 H N N 384 TYR HD1 H N N 385 TYR HD2 H N N 386 TYR HE1 H N N 387 TYR HE2 H N N 388 TYR HH H N N 389 TYR HXT H N N 390 VAL N N N N 391 VAL CA C N S 392 VAL C C N N 393 VAL O O N N 394 VAL CB C N N 395 VAL CG1 C N N 396 VAL CG2 C N N 397 VAL OXT O N N 398 VAL H H N N 399 VAL H2 H N N 400 VAL HA H N N 401 VAL HB H N N 402 VAL HG11 H N N 403 VAL HG12 H N N 404 VAL HG13 H N N 405 VAL HG21 H N N 406 VAL HG22 H N N 407 VAL HG23 H N N 408 VAL HXT H N N 409 # 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 GOL C1 O1 sing N N 129 GOL C1 C2 sing N N 130 GOL C1 H11 sing N N 131 GOL C1 H12 sing N N 132 GOL O1 HO1 sing N N 133 GOL C2 O2 sing N N 134 GOL C2 C3 sing N N 135 GOL C2 H2 sing N N 136 GOL O2 HO2 sing N N 137 GOL C3 O3 sing N N 138 GOL C3 H31 sing N N 139 GOL C3 H32 sing N N 140 GOL O3 HO3 sing N N 141 HIS N CA sing N N 142 HIS N H sing N N 143 HIS N H2 sing N N 144 HIS CA C sing N N 145 HIS CA CB sing N N 146 HIS CA HA sing N N 147 HIS C O doub N N 148 HIS C OXT sing N N 149 HIS CB CG sing N N 150 HIS CB HB2 sing N N 151 HIS CB HB3 sing N N 152 HIS CG ND1 sing Y N 153 HIS CG CD2 doub Y N 154 HIS ND1 CE1 doub Y N 155 HIS ND1 HD1 sing N N 156 HIS CD2 NE2 sing Y N 157 HIS CD2 HD2 sing N N 158 HIS CE1 NE2 sing Y N 159 HIS CE1 HE1 sing N N 160 HIS NE2 HE2 sing N N 161 HIS OXT HXT sing N N 162 HOH O H1 sing N N 163 HOH O H2 sing N N 164 ILE N CA sing N N 165 ILE N H sing N N 166 ILE N H2 sing N N 167 ILE CA C sing N N 168 ILE CA CB sing N N 169 ILE CA HA sing N N 170 ILE C O doub N N 171 ILE C OXT sing N N 172 ILE CB CG1 sing N N 173 ILE CB CG2 sing N N 174 ILE CB HB sing N N 175 ILE CG1 CD1 sing N N 176 ILE CG1 HG12 sing N N 177 ILE CG1 HG13 sing N N 178 ILE CG2 HG21 sing N N 179 ILE CG2 HG22 sing N N 180 ILE CG2 HG23 sing N N 181 ILE CD1 HD11 sing N N 182 ILE CD1 HD12 sing N N 183 ILE CD1 HD13 sing N N 184 ILE OXT HXT sing N N 185 LEU N CA sing N N 186 LEU N H sing N N 187 LEU N H2 sing N N 188 LEU CA C sing N N 189 LEU CA CB sing N N 190 LEU CA HA sing N N 191 LEU C O doub N N 192 LEU C OXT sing N N 193 LEU CB CG sing N N 194 LEU CB HB2 sing N N 195 LEU CB HB3 sing N N 196 LEU CG CD1 sing N N 197 LEU CG CD2 sing N N 198 LEU CG HG sing N N 199 LEU CD1 HD11 sing N N 200 LEU CD1 HD12 sing N N 201 LEU CD1 HD13 sing N N 202 LEU CD2 HD21 sing N N 203 LEU CD2 HD22 sing N N 204 LEU CD2 HD23 sing N N 205 LEU OXT HXT sing N N 206 LYS N CA sing N N 207 LYS N H sing N N 208 LYS N H2 sing N N 209 LYS CA C sing N N 210 LYS CA CB sing N N 211 LYS CA HA sing N N 212 LYS C O doub N N 213 LYS C OXT sing N N 214 LYS CB CG sing N N 215 LYS CB HB2 sing N N 216 LYS CB HB3 sing N N 217 LYS CG CD sing N N 218 LYS CG HG2 sing N N 219 LYS CG HG3 sing N N 220 LYS CD CE sing N N 221 LYS CD HD2 sing N N 222 LYS CD HD3 sing N N 223 LYS CE NZ sing N N 224 LYS CE HE2 sing N N 225 LYS CE HE3 sing N N 226 LYS NZ HZ1 sing N N 227 LYS NZ HZ2 sing N N 228 LYS NZ HZ3 sing N N 229 LYS OXT HXT sing N N 230 MET N CA sing N N 231 MET N H sing N N 232 MET N H2 sing N N 233 MET CA C sing N N 234 MET CA CB sing N N 235 MET CA HA sing N N 236 MET C O doub N N 237 MET C OXT sing N N 238 MET CB CG sing N N 239 MET CB HB2 sing N N 240 MET CB HB3 sing N N 241 MET CG SD sing N N 242 MET CG HG2 sing N N 243 MET CG HG3 sing N N 244 MET SD CE sing N N 245 MET CE HE1 sing N N 246 MET CE HE2 sing N N 247 MET CE HE3 sing N N 248 MET OXT HXT sing N N 249 PHE N CA sing N N 250 PHE N H sing N N 251 PHE N H2 sing N N 252 PHE CA C sing N N 253 PHE CA CB sing N N 254 PHE CA HA sing N N 255 PHE C O doub N N 256 PHE C OXT sing N N 257 PHE CB CG sing N N 258 PHE CB HB2 sing N N 259 PHE CB HB3 sing N N 260 PHE CG CD1 doub Y N 261 PHE CG CD2 sing Y N 262 PHE CD1 CE1 sing Y N 263 PHE CD1 HD1 sing N N 264 PHE CD2 CE2 doub Y N 265 PHE CD2 HD2 sing N N 266 PHE CE1 CZ doub Y N 267 PHE CE1 HE1 sing N N 268 PHE CE2 CZ sing Y N 269 PHE CE2 HE2 sing N N 270 PHE CZ HZ sing N N 271 PHE OXT HXT sing N N 272 PRO N CA sing N N 273 PRO N CD sing N N 274 PRO N H sing N N 275 PRO CA C sing N N 276 PRO CA CB sing N N 277 PRO CA HA sing N N 278 PRO C O doub N N 279 PRO C OXT sing N N 280 PRO CB CG sing N N 281 PRO CB HB2 sing N N 282 PRO CB HB3 sing N N 283 PRO CG CD sing N N 284 PRO CG HG2 sing N N 285 PRO CG HG3 sing N N 286 PRO CD HD2 sing N N 287 PRO CD HD3 sing N N 288 PRO OXT HXT sing N N 289 SER N CA sing N N 290 SER N H sing N N 291 SER N H2 sing N N 292 SER CA C sing N N 293 SER CA CB sing N N 294 SER CA HA sing N N 295 SER C O doub N N 296 SER C OXT sing N N 297 SER CB OG sing N N 298 SER CB HB2 sing N N 299 SER CB HB3 sing N N 300 SER OG HG sing N N 301 SER OXT HXT sing N N 302 SO4 S O1 doub N N 303 SO4 S O2 doub N N 304 SO4 S O3 sing N N 305 SO4 S O4 sing N N 306 THR N CA sing N N 307 THR N H sing N N 308 THR N H2 sing N N 309 THR CA C sing N N 310 THR CA CB sing N N 311 THR CA HA sing N N 312 THR C O doub N N 313 THR C OXT sing N N 314 THR CB OG1 sing N N 315 THR CB CG2 sing N N 316 THR CB HB sing N N 317 THR OG1 HG1 sing N N 318 THR CG2 HG21 sing N N 319 THR CG2 HG22 sing N N 320 THR CG2 HG23 sing N N 321 THR OXT HXT sing N N 322 TRP N CA sing N N 323 TRP N H sing N N 324 TRP N H2 sing N N 325 TRP CA C sing N N 326 TRP CA CB sing N N 327 TRP CA HA sing N N 328 TRP C O doub N N 329 TRP C OXT sing N N 330 TRP CB CG sing N N 331 TRP CB HB2 sing N N 332 TRP CB HB3 sing N N 333 TRP CG CD1 doub Y N 334 TRP CG CD2 sing Y N 335 TRP CD1 NE1 sing Y N 336 TRP CD1 HD1 sing N N 337 TRP CD2 CE2 doub Y N 338 TRP CD2 CE3 sing Y N 339 TRP NE1 CE2 sing Y N 340 TRP NE1 HE1 sing N N 341 TRP CE2 CZ2 sing Y N 342 TRP CE3 CZ3 doub Y N 343 TRP CE3 HE3 sing N N 344 TRP CZ2 CH2 doub Y N 345 TRP CZ2 HZ2 sing N N 346 TRP CZ3 CH2 sing Y N 347 TRP CZ3 HZ3 sing N N 348 TRP CH2 HH2 sing N N 349 TRP OXT HXT sing N N 350 TYR N CA sing N N 351 TYR N H sing N N 352 TYR N H2 sing N N 353 TYR CA C sing N N 354 TYR CA CB sing N N 355 TYR CA HA sing N N 356 TYR C O doub N N 357 TYR C OXT sing N N 358 TYR CB CG sing N N 359 TYR CB HB2 sing N N 360 TYR CB HB3 sing N N 361 TYR CG CD1 doub Y N 362 TYR CG CD2 sing Y N 363 TYR CD1 CE1 sing Y N 364 TYR CD1 HD1 sing N N 365 TYR CD2 CE2 doub Y N 366 TYR CD2 HD2 sing N N 367 TYR CE1 CZ doub Y N 368 TYR CE1 HE1 sing N N 369 TYR CE2 CZ sing Y N 370 TYR CE2 HE2 sing N N 371 TYR CZ OH sing N N 372 TYR OH HH sing N N 373 TYR OXT HXT sing N N 374 VAL N CA sing N N 375 VAL N H sing N N 376 VAL N H2 sing N N 377 VAL CA C sing N N 378 VAL CA CB sing N N 379 VAL CA HA sing N N 380 VAL C O doub N N 381 VAL C OXT sing N N 382 VAL CB CG1 sing N N 383 VAL CB CG2 sing N N 384 VAL CB HB sing N N 385 VAL CG1 HG11 sing N N 386 VAL CG1 HG12 sing N N 387 VAL CG1 HG13 sing N N 388 VAL CG2 HG21 sing N N 389 VAL CG2 HG22 sing N N 390 VAL CG2 HG23 sing N N 391 VAL OXT HXT sing N N 392 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 'SULFATE ION' SO4 4 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 1W1D _pdbx_initial_refinement_model.details 'PDB ENTRY 1W1D' #