data_4XLV # _model_server_result.job_id LuVijK20ncvNTM1b29eLjg _model_server_result.datetime_utc '2025-08-03 04:49:15' _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 4xlv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1301}' # _entry.id 4XLV # _exptl.entry_id 4XLV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4XLV _cell.length_a 66.982 _cell.length_b 66.982 _cell.length_c 136.58 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 136.58 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C ILE 202 A ILE 1157 1_555 A N PTR 203 A PTR 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C PTR 203 A PTR 1158 1_555 A N GLU 204 A GLU 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C ASP 206 A ASP 1161 1_555 A N PTR 207 A PTR 1162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C PTR 207 A PTR 1162 1_555 A N PTR 208 A PTR 1163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C PTR 208 A PTR 1163 1_555 A N ARG 209 A ARG 1164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A OD1 ASN 182 A ASN 1137 1_555 C MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 A OD2 ASP 195 A ASP 1150 1_555 C MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 B O1B ACP . A ACP 1301 1_555 C MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc4 B O1A ACP . A ACP 1301 1_555 C MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc5 B O3G ACP . A ACP 1301 1_555 D MG MG . A MG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc6 B O2B ACP . A ACP 1301 1_555 D MG MG . A MG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc7 C MG MG . A MG 1302 1_555 E O HOH . A HOH 1456 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc8 D MG MG . A MG 1303 1_555 E O HOH . A HOH 1478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc9 D MG MG . A MG 1303 1_555 E O HOH . A HOH 1487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 4XLV _atom_sites.fract_transf_matrix[1][1] 0.014929 _atom_sites.fract_transf_matrix[1][2] 0.008619 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017239 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007322 _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 B 2 ACP A 1 1301 200 ACP ACP . C 3 MG A 1 1302 201 MG MG . D 3 MG A 1 1303 202 MG MG . E 4 HOH A 1 1401 51 HOH HOH . E 4 HOH A 2 1402 125 HOH HOH . E 4 HOH A 3 1403 54 HOH HOH . E 4 HOH A 4 1404 80 HOH HOH . E 4 HOH A 5 1405 138 HOH HOH . E 4 HOH A 6 1406 11 HOH HOH . E 4 HOH A 7 1407 142 HOH HOH . E 4 HOH A 8 1408 69 HOH HOH . E 4 HOH A 9 1409 143 HOH HOH . E 4 HOH A 10 1410 17 HOH HOH . E 4 HOH A 11 1411 127 HOH HOH . E 4 HOH A 12 1412 47 HOH HOH . E 4 HOH A 13 1413 73 HOH HOH . E 4 HOH A 14 1414 18 HOH HOH . E 4 HOH A 15 1415 62 HOH HOH . E 4 HOH A 16 1416 128 HOH HOH . E 4 HOH A 17 1417 93 HOH HOH . E 4 HOH A 18 1418 116 HOH HOH . E 4 HOH A 19 1419 8 HOH HOH . E 4 HOH A 20 1420 95 HOH HOH . E 4 HOH A 21 1421 27 HOH HOH . E 4 HOH A 22 1422 63 HOH HOH . E 4 HOH A 23 1423 85 HOH HOH . E 4 HOH A 24 1424 99 HOH HOH . E 4 HOH A 25 1425 106 HOH HOH . E 4 HOH A 26 1426 123 HOH HOH . E 4 HOH A 27 1427 94 HOH HOH . E 4 HOH A 28 1428 77 HOH HOH . E 4 HOH A 29 1429 119 HOH HOH . E 4 HOH A 30 1430 98 HOH HOH . E 4 HOH A 31 1431 1 HOH HOH . E 4 HOH A 32 1432 2 HOH HOH . E 4 HOH A 33 1433 3 HOH HOH . E 4 HOH A 34 1434 4 HOH HOH . E 4 HOH A 35 1435 5 HOH HOH . E 4 HOH A 36 1436 6 HOH HOH . E 4 HOH A 37 1437 7 HOH HOH . E 4 HOH A 38 1438 9 HOH HOH . E 4 HOH A 39 1439 10 HOH HOH . E 4 HOH A 40 1440 12 HOH HOH . E 4 HOH A 41 1441 13 HOH HOH . E 4 HOH A 42 1442 14 HOH HOH . E 4 HOH A 43 1443 15 HOH HOH . E 4 HOH A 44 1444 16 HOH HOH . E 4 HOH A 45 1445 19 HOH HOH . E 4 HOH A 46 1446 20 HOH HOH . E 4 HOH A 47 1447 21 HOH HOH . E 4 HOH A 48 1448 22 HOH HOH . E 4 HOH A 49 1449 23 HOH HOH . E 4 HOH A 50 1450 24 HOH HOH . E 4 HOH A 51 1451 25 HOH HOH . E 4 HOH A 52 1452 26 HOH HOH . E 4 HOH A 53 1453 28 HOH HOH . E 4 HOH A 54 1454 29 HOH HOH . E 4 HOH A 55 1455 30 HOH HOH . E 4 HOH A 56 1456 31 HOH HOH . E 4 HOH A 57 1457 32 HOH HOH . E 4 HOH A 58 1458 33 HOH HOH . E 4 HOH A 59 1459 34 HOH HOH . E 4 HOH A 60 1460 35 HOH HOH . E 4 HOH A 61 1461 36 HOH HOH . E 4 HOH A 62 1462 37 HOH HOH . E 4 HOH A 63 1463 38 HOH HOH . E 4 HOH A 64 1464 39 HOH HOH . E 4 HOH A 65 1465 40 HOH HOH . E 4 HOH A 66 1466 41 HOH HOH . E 4 HOH A 67 1467 42 HOH HOH . E 4 HOH A 68 1468 43 HOH HOH . E 4 HOH A 69 1469 44 HOH HOH . E 4 HOH A 70 1470 45 HOH HOH . E 4 HOH A 71 1471 46 HOH HOH . E 4 HOH A 72 1472 48 HOH HOH . E 4 HOH A 73 1473 49 HOH HOH . E 4 HOH A 74 1474 50 HOH HOH . E 4 HOH A 75 1475 52 HOH HOH . E 4 HOH A 76 1476 53 HOH HOH . E 4 HOH A 77 1477 55 HOH HOH . E 4 HOH A 78 1478 56 HOH HOH . E 4 HOH A 79 1479 57 HOH HOH . E 4 HOH A 80 1480 58 HOH HOH . E 4 HOH A 81 1481 59 HOH HOH . E 4 HOH A 82 1482 60 HOH HOH . E 4 HOH A 83 1483 61 HOH HOH . E 4 HOH A 84 1484 64 HOH HOH . E 4 HOH A 85 1485 65 HOH HOH . E 4 HOH A 86 1486 66 HOH HOH . E 4 HOH A 87 1487 67 HOH HOH . E 4 HOH A 88 1488 68 HOH HOH . E 4 HOH A 89 1489 70 HOH HOH . E 4 HOH A 90 1490 71 HOH HOH . E 4 HOH A 91 1491 72 HOH HOH . E 4 HOH A 92 1492 74 HOH HOH . E 4 HOH A 93 1493 75 HOH HOH . E 4 HOH A 94 1494 76 HOH HOH . E 4 HOH A 95 1495 79 HOH HOH . E 4 HOH A 96 1496 81 HOH HOH . E 4 HOH A 97 1497 82 HOH HOH . E 4 HOH A 98 1498 83 HOH HOH . E 4 HOH A 99 1499 84 HOH HOH . E 4 HOH A 100 1500 86 HOH HOH . E 4 HOH A 101 1501 87 HOH HOH . E 4 HOH A 102 1502 88 HOH HOH . E 4 HOH A 103 1503 89 HOH HOH . E 4 HOH A 104 1504 90 HOH HOH . E 4 HOH A 105 1505 91 HOH HOH . E 4 HOH A 106 1506 92 HOH HOH . E 4 HOH A 107 1507 96 HOH HOH . E 4 HOH A 108 1508 97 HOH HOH . E 4 HOH A 109 1509 100 HOH HOH . E 4 HOH A 110 1510 101 HOH HOH . E 4 HOH A 111 1511 102 HOH HOH . E 4 HOH A 112 1512 103 HOH HOH . E 4 HOH A 113 1513 104 HOH HOH . E 4 HOH A 114 1514 105 HOH HOH . E 4 HOH A 115 1515 108 HOH HOH . E 4 HOH A 116 1516 109 HOH HOH . E 4 HOH A 117 1517 110 HOH HOH . E 4 HOH A 118 1518 111 HOH HOH . E 4 HOH A 119 1519 112 HOH HOH . E 4 HOH A 120 1520 113 HOH HOH . E 4 HOH A 121 1521 114 HOH HOH . E 4 HOH A 122 1522 115 HOH HOH . E 4 HOH A 123 1523 117 HOH HOH . E 4 HOH A 124 1524 118 HOH HOH . E 4 HOH A 125 1525 120 HOH HOH . E 4 HOH A 126 1526 121 HOH HOH . E 4 HOH A 127 1527 122 HOH HOH . E 4 HOH A 128 1528 124 HOH HOH . E 4 HOH A 129 1529 126 HOH HOH . E 4 HOH A 130 1530 129 HOH HOH . E 4 HOH A 131 1531 130 HOH HOH . E 4 HOH A 132 1532 131 HOH HOH . E 4 HOH A 133 1533 132 HOH HOH . E 4 HOH A 134 1534 133 HOH HOH . E 4 HOH A 135 1535 134 HOH HOH . E 4 HOH A 136 1536 135 HOH HOH . E 4 HOH A 137 1537 136 HOH HOH . E 4 HOH A 138 1538 137 HOH HOH . E 4 HOH A 139 1539 139 HOH HOH . E 4 HOH A 140 1540 140 HOH HOH . E 4 HOH A 141 1541 141 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 PG ACP . . . B 2 27.487 10.247 56.446 1 51.93 ? PG ACP 1301 A 1 HETATM 2 O O1G ACP . . . B 2 27.451 9.164 55.419 1 42.92 ? O1G ACP 1301 A 1 HETATM 3 O O2G ACP . . . B 2 26.04 10.995 56.498 1 42.26 ? O2G ACP 1301 A 1 HETATM 4 O O3G ACP . . . B 2 28.673 11.318 56.179 1 46.64 ? O3G ACP 1301 A 1 HETATM 5 P PB ACP . . . B 2 29.268 8.525 58.197 1 37.03 ? PB ACP 1301 A 1 HETATM 6 O O1B ACP . . . B 2 29.391 7.505 57.141 1 32.73 ? O1B ACP 1301 A 1 HETATM 7 O O2B ACP . . . B 2 30.568 9.483 58.273 1 38.39 ? O2B ACP 1301 A 1 HETATM 8 C C3B ACP . . . B 2 27.758 9.494 58.071 1 39.38 ? C3B ACP 1301 A 1 HETATM 9 P PA ACP . . . B 2 28.056 6.741 60.118 1 36.37 ? PA ACP 1301 A 1 HETATM 10 O O1A ACP . . . B 2 27.634 5.808 59.001 1 32.62 ? O1A ACP 1301 A 1 HETATM 11 O O2A ACP . . . B 2 26.986 7.436 60.917 1 34.13 ? O2A ACP 1301 A 1 HETATM 12 O O3A ACP . . . B 2 29.202 7.784 59.625 1 38.76 ? O3A ACP 1301 A 1 HETATM 13 O O5' ACP . . . B 2 29.05 6.008 61.152 1 35.81 ? O5' ACP 1301 A 1 HETATM 14 C C5' ACP . . . B 2 30.443 5.915 60.854 1 34.4 ? C5' ACP 1301 A 1 HETATM 15 C C4' ACP . . . B 2 30.935 4.749 61.702 1 34.31 ? C4' ACP 1301 A 1 HETATM 16 O O4' ACP . . . B 2 30.892 5.12 63.086 1 33.24 ? O4' ACP 1301 A 1 HETATM 17 C C3' ACP . . . B 2 29.999 3.566 61.553 1 31.52 ? C3' ACP 1301 A 1 HETATM 18 O O3' ACP . . . B 2 30.413 2.729 60.469 1 35.06 ? O3' ACP 1301 A 1 HETATM 19 C C2' ACP . . . B 2 30.005 2.911 62.925 1 31.98 ? C2' ACP 1301 A 1 HETATM 20 O O2' ACP . . . B 2 30.975 1.865 63.101 1 31.76 ? O2' ACP 1301 A 1 HETATM 21 C C1' ACP . . . B 2 30.288 4.086 63.856 1 30.59 ? C1' ACP 1301 A 1 HETATM 22 N N9 ACP . . . B 2 28.951 4.495 64.336 1 27.71 ? N9 ACP 1301 A 1 HETATM 23 C C8 ACP . . . B 2 28.058 5.297 63.726 1 26.66 ? C8 ACP 1301 A 1 HETATM 24 N N7 ACP . . . B 2 26.92 5.405 64.455 1 26.79 ? N7 ACP 1301 A 1 HETATM 25 C C5 ACP . . . B 2 27.076 4.64 65.552 1 26.18 ? C5 ACP 1301 A 1 HETATM 26 C C6 ACP . . . B 2 26.286 4.291 66.745 1 24.3 ? C6 ACP 1301 A 1 HETATM 27 N N6 ACP . . . B 2 25.05 4.778 66.957 1 23.65 ? N6 ACP 1301 A 1 HETATM 28 N N1 ACP . . . B 2 26.827 3.455 67.632 1 23.96 ? N1 ACP 1301 A 1 HETATM 29 C C2 ACP . . . B 2 28.059 2.95 67.473 1 25.62 ? C2 ACP 1301 A 1 HETATM 30 N N3 ACP . . . B 2 28.843 3.223 66.433 1 24.17 ? N3 ACP 1301 A 1 HETATM 31 C C4 ACP . . . B 2 28.41 4.037 65.457 1 26.23 ? C4 ACP 1301 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #