data_6GR2 # _model_server_result.job_id Vs3eL3RwRHNSRWky1RCN8g _model_server_result.datetime_utc '2025-07-27 12:39:14' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6gr2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":402}' # _entry.id 6GR2 # _exptl.entry_id 6GR2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 113.85 _cell.angle_beta 102.26 _cell.angle_gamma 101.29 _cell.entry_id 6GR2 _cell.length_a 78.217 _cell.length_b 110.32 _cell.length_c 118.234 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GR2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,F,I,J,V,W,X,DA,IA 1 1 B,K,L,M,N,EA 2 1 C,O,P,Q,FA 2 2 D,G,R,S,Y,Z,GA,JA 3 1 E,H,T,U,AA,BA,CA,HA,KA 4 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_455 x-1,y,z 1 0 0 0 1 0 0 0 1 -78.217 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 J N N ? 3 L N N ? 3 P N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Z N N ? 3 BA N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 398 A CYS 391 1_555 F SG CYS 398 F CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 398 B CYS 391 1_555 C SG CYS 398 C CYS 391 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 D SG CYS 398 D CYS 391 1_555 G SG CYS 398 G CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 E SG CYS 398 E CYS 391 1_555 H SG CYS 398 H CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6GR2 _atom_sites.fract_transf_matrix[1][1] 0.012785 _atom_sites.fract_transf_matrix[1][2] 0.002552 _atom_sites.fract_transf_matrix[1][3] 0.004481 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009243 _atom_sites.fract_transf_matrix[2][3] 0.004859 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009778 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code I 2 GAL A 1 401 393 GAL GAL . J 3 ADP A 1 402 401 ADP ADP . K 2 GAL B 1 401 393 GAL GAL . L 3 ADP B 1 402 401 ADP ADP . M 4 SO4 B 1 403 501 SO4 SO4 . N 4 SO4 B 1 404 601 SO4 SO4 . O 2 GAL C 1 401 393 GAL GAL . P 3 ADP C 1 402 401 ADP ADP . Q 4 SO4 C 1 403 501 SO4 SO4 . R 2 GAL D 1 401 393 GAL GAL . S 3 ADP D 1 402 401 ADP ADP . T 2 GAL E 1 401 393 GAL GAL . U 3 ADP E 1 402 401 ADP ADP . V 2 GAL F 1 401 393 GAL GAL . W 3 ADP F 1 402 401 ADP ADP . X 4 SO4 F 1 403 501 SO4 SO4 . Y 2 GAL G 1 401 393 GAL GAL . Z 3 ADP G 1 402 401 ADP ADP . AA 2 GAL H 1 401 393 GAL GAL . BA 3 ADP H 1 402 401 ADP ADP . CA 4 SO4 H 1 403 501 SO4 SO4 . DA 5 HOH A 1 501 13 HOH HOH . DA 5 HOH A 2 502 30 HOH HOH . DA 5 HOH A 3 503 24 HOH HOH . DA 5 HOH A 4 504 28 HOH HOH . DA 5 HOH A 5 505 29 HOH HOH . DA 5 HOH A 6 506 20 HOH HOH . DA 5 HOH A 7 507 23 HOH HOH . DA 5 HOH A 8 508 26 HOH HOH . DA 5 HOH A 9 509 27 HOH HOH . DA 5 HOH A 10 510 115 HOH HOH . EA 5 HOH B 1 501 40 HOH HOH . EA 5 HOH B 2 502 44 HOH HOH . EA 5 HOH B 3 503 33 HOH HOH . EA 5 HOH B 4 504 35 HOH HOH . EA 5 HOH B 5 505 14 HOH HOH . EA 5 HOH B 6 506 17 HOH HOH . EA 5 HOH B 7 507 37 HOH HOH . EA 5 HOH B 8 508 41 HOH HOH . EA 5 HOH B 9 509 34 HOH HOH . EA 5 HOH B 10 510 36 HOH HOH . EA 5 HOH B 11 511 16 HOH HOH . EA 5 HOH B 12 512 18 HOH HOH . EA 5 HOH B 13 513 38 HOH HOH . EA 5 HOH B 14 514 32 HOH HOH . EA 5 HOH B 15 515 31 HOH HOH . EA 5 HOH B 16 516 42 HOH HOH . EA 5 HOH B 17 517 43 HOH HOH . FA 5 HOH C 1 501 48 HOH HOH . FA 5 HOH C 2 502 52 HOH HOH . FA 5 HOH C 3 503 110 HOH HOH . FA 5 HOH C 4 504 50 HOH HOH . FA 5 HOH C 5 505 12 HOH HOH . FA 5 HOH C 6 506 47 HOH HOH . FA 5 HOH C 7 507 49 HOH HOH . FA 5 HOH C 8 508 54 HOH HOH . FA 5 HOH C 9 509 51 HOH HOH . FA 5 HOH C 10 510 45 HOH HOH . GA 5 HOH D 1 501 55 HOH HOH . GA 5 HOH D 2 502 21 HOH HOH . GA 5 HOH D 3 503 53 HOH HOH . GA 5 HOH D 4 504 62 HOH HOH . GA 5 HOH D 5 505 59 HOH HOH . GA 5 HOH D 6 506 57 HOH HOH . GA 5 HOH D 7 507 61 HOH HOH . GA 5 HOH D 8 508 58 HOH HOH . GA 5 HOH D 9 509 2 HOH HOH . GA 5 HOH D 10 510 15 HOH HOH . GA 5 HOH D 11 511 60 HOH HOH . HA 5 HOH E 1 501 106 HOH HOH . HA 5 HOH E 2 502 71 HOH HOH . HA 5 HOH E 3 503 10 HOH HOH . HA 5 HOH E 4 504 74 HOH HOH . HA 5 HOH E 5 505 66 HOH HOH . HA 5 HOH E 6 506 67 HOH HOH . HA 5 HOH E 7 507 65 HOH HOH . HA 5 HOH E 8 508 73 HOH HOH . HA 5 HOH E 9 509 64 HOH HOH . HA 5 HOH E 10 510 69 HOH HOH . HA 5 HOH E 11 511 63 HOH HOH . HA 5 HOH E 12 512 70 HOH HOH . HA 5 HOH E 13 513 75 HOH HOH . HA 5 HOH E 14 514 72 HOH HOH . IA 5 HOH F 1 501 87 HOH HOH . IA 5 HOH F 2 502 83 HOH HOH . IA 5 HOH F 3 503 82 HOH HOH . IA 5 HOH F 4 504 19 HOH HOH . IA 5 HOH F 5 505 84 HOH HOH . IA 5 HOH F 6 506 76 HOH HOH . IA 5 HOH F 7 507 88 HOH HOH . IA 5 HOH F 8 508 85 HOH HOH . IA 5 HOH F 9 509 25 HOH HOH . IA 5 HOH F 10 510 91 HOH HOH . IA 5 HOH F 11 511 81 HOH HOH . IA 5 HOH F 12 512 68 HOH HOH . IA 5 HOH F 13 513 79 HOH HOH . IA 5 HOH F 14 514 4 HOH HOH . IA 5 HOH F 15 515 78 HOH HOH . IA 5 HOH F 16 516 92 HOH HOH . IA 5 HOH F 17 517 86 HOH HOH . IA 5 HOH F 18 518 89 HOH HOH . IA 5 HOH F 19 519 80 HOH HOH . IA 5 HOH F 20 520 77 HOH HOH . JA 5 HOH G 1 501 93 HOH HOH . JA 5 HOH G 2 502 97 HOH HOH . JA 5 HOH G 3 503 94 HOH HOH . JA 5 HOH G 4 504 6 HOH HOH . JA 5 HOH G 5 505 1 HOH HOH . JA 5 HOH G 6 506 95 HOH HOH . JA 5 HOH G 7 507 98 HOH HOH . JA 5 HOH G 8 508 99 HOH HOH . JA 5 HOH G 9 509 96 HOH HOH . KA 5 HOH H 1 501 103 HOH HOH . KA 5 HOH H 2 502 109 HOH HOH . KA 5 HOH H 3 503 113 HOH HOH . KA 5 HOH H 4 504 108 HOH HOH . KA 5 HOH H 5 505 104 HOH HOH . KA 5 HOH H 6 506 114 HOH HOH . KA 5 HOH H 7 507 8 HOH HOH . KA 5 HOH H 8 508 101 HOH HOH . KA 5 HOH H 9 509 105 HOH HOH . KA 5 HOH H 10 510 112 HOH HOH . KA 5 HOH H 11 511 9 HOH HOH . KA 5 HOH H 12 512 111 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . W 3 -85.08 21.521 44.183 1 40.46 ? PB ADP 402 F 1 HETATM 2 O O1B ADP . . . W 3 -83.887 21.898 43.344 1 38.52 ? O1B ADP 402 F 1 HETATM 3 O O2B ADP . . . W 3 -85.547 20.101 43.988 1 42.1 ? O2B ADP 402 F 1 HETATM 4 O O3B ADP . . . W 3 -84.963 21.946 45.624 1 47.25 ? O3B ADP 402 F 1 HETATM 5 P PA ADP . . . W 3 -86.051 23.873 42.886 1 47.71 ? PA ADP 402 F 1 HETATM 6 O O1A ADP . . . W 3 -84.621 24.287 43 1 55.89 ? O1A ADP 402 F 1 HETATM 7 O O2A ADP . . . W 3 -87.097 24.788 43.454 1 47.64 ? O2A ADP 402 F 1 HETATM 8 O O3A ADP . . . W 3 -86.285 22.42 43.596 1 43.67 ? O3A ADP 402 F 1 HETATM 9 O O5' ADP . . . W 3 -86.39 23.623 41.341 1 53.47 ? O5' ADP 402 F 1 HETATM 10 C C5' ADP . . . W 3 -86.478 22.295 40.805 1 58.72 ? C5' ADP 402 F 1 HETATM 11 C C4' ADP . . . W 3 -87.062 22.635 39.422 1 61.71 ? C4' ADP 402 F 1 HETATM 12 O O4' ADP . . . W 3 -86.037 22.378 38.419 1 61.13 ? O4' ADP 402 F 1 HETATM 13 C C3' ADP . . . W 3 -88.475 22.105 39.048 1 62.15 ? C3' ADP 402 F 1 HETATM 14 O O3' ADP . . . W 3 -89.463 23.175 39.1 1 65.47 ? O3' ADP 402 F 1 HETATM 15 C C2' ADP . . . W 3 -88.121 21.613 37.632 1 61.36 ? C2' ADP 402 F 1 HETATM 16 O O2' ADP . . . W 3 -88.796 22.403 36.664 1 63.21 ? O2' ADP 402 F 1 HETATM 17 C C1' ADP . . . W 3 -86.602 21.696 37.313 1 60.73 ? C1' ADP 402 F 1 HETATM 18 N N9 ADP . . . W 3 -86.192 20.28 37.241 1 60.06 ? N9 ADP 402 F 1 HETATM 19 C C8 ADP . . . W 3 -85.553 19.678 38.254 1 59.76 ? C8 ADP 402 F 1 HETATM 20 N N7 ADP . . . W 3 -85.328 18.367 37.98 1 60.87 ? N7 ADP 402 F 1 HETATM 21 C C5 ADP . . . W 3 -85.835 18.094 36.768 1 60.42 ? C5 ADP 402 F 1 HETATM 22 C C6 ADP . . . W 3 -85.916 16.882 35.911 1 59.11 ? C6 ADP 402 F 1 HETATM 23 N N6 ADP . . . W 3 -85.394 15.7 36.33 1 60.16 ? N6 ADP 402 F 1 HETATM 24 N N1 ADP . . . W 3 -86.525 17.001 34.711 1 59.78 ? N1 ADP 402 F 1 HETATM 25 C C2 ADP . . . W 3 -87.041 18.176 34.297 1 60.03 ? C2 ADP 402 F 1 HETATM 26 N N3 ADP . . . W 3 -86.994 19.312 35.037 1 58.8 ? N3 ADP 402 F 1 HETATM 27 C C4 ADP . . . W 3 -86.411 19.358 36.268 1 59.8 ? C4 ADP 402 F 1 HETATM 28 H "H5'1" ADP . . . W 3 -87.137 21.651 41.391 1 70.46 ? "H5'1" ADP 402 F 1 HETATM 29 H "H5'2" ADP . . . W 3 -85.503 21.806 40.739 1 70.46 ? "H5'2" ADP 402 F 1 HETATM 30 H H4' ADP . . . W 3 -87.309 23.705 39.462 1 74.06 ? H4' ADP 402 F 1 HETATM 31 H H3' ADP . . . W 3 -88.941 21.349 39.695 1 74.58 ? H3' ADP 402 F 1 HETATM 32 H HO3' ADP . . . W 3 -89.195 23.891 38.508 1 78.56 ? HO3' ADP 402 F 1 HETATM 33 H H2' ADP . . . W 3 -88.433 20.56 37.592 1 73.64 ? H2' ADP 402 F 1 HETATM 34 H HO2' ADP . . . W 3 -88.616 23.339 36.829 1 75.85 ? HO2' ADP 402 F 1 HETATM 35 H H1' ADP . . . W 3 -86.319 22.221 36.39 1 72.87 ? H1' ADP 402 F 1 HETATM 36 H H8 ADP . . . W 3 -85.256 20.172 39.171 1 71.71 ? H8 ADP 402 F 1 HETATM 37 H HN61 ADP . . . W 3 -85.456 14.883 35.738 1 72.19 ? HN61 ADP 402 F 1 HETATM 38 H HN62 ADP . . . W 3 -84.944 15.637 37.232 1 72.19 ? HN62 ADP 402 F 1 HETATM 39 H H2 ADP . . . W 3 -87.516 18.215 33.325 1 72.04 ? H2 ADP 402 F 1 # _model_server_stats.io_time_ms 292 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #