data_3VYW # _model_server_result.job_id iprEeVzp6bl7kkB32NKdWA _model_server_result.datetime_utc '2024-11-04 22:51:52' _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 3vyw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 3VYW # _exptl.entry_id 3VYW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.44 _cell.angle_gamma 90 _cell.entry_id 3VYW _cell.length_a 55.487 _cell.length_b 107.581 _cell.length_c 117.711 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VYW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 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,E,K 1 1 B,F,G,L 2 1 C,H,I,M 3 1 D,J,N 4 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 H N N ? 2 J 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 covale ? covale1 A C PRO 265 A PRO 265 1_555 A N MSE 266 A MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale2 A C MSE 266 A MSE 266 1_555 A N GLU 267 A GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? covale ? covale3 A C PRO 282 A PRO 282 1_555 A N MSE 283 A MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.246 ? covale ? covale4 A C MSE 283 A MSE 283 1_555 A N ARG 284 A ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 B C PRO 265 B PRO 265 1_555 B N MSE 266 B MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale6 B C MSE 266 B MSE 266 1_555 B N GLU 267 B GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.255 ? covale ? covale7 B C PRO 282 B PRO 282 1_555 B N MSE 283 B MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.276 ? covale ? covale8 B C MSE 283 B MSE 283 1_555 B N ARG 284 B ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 C C PRO 265 C PRO 265 1_555 C N MSE 266 C MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? covale ? covale10 C C MSE 266 C MSE 266 1_555 C N GLU 267 C GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.251 ? covale ? covale11 C C PRO 282 C PRO 282 1_555 C N MSE 283 C MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.26 ? covale ? covale12 C C MSE 283 C MSE 283 1_555 C N ARG 284 C ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.263 ? covale ? covale13 D C PRO 265 D PRO 265 1_555 D N MSE 266 D MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? covale ? covale14 D C MSE 266 D MSE 266 1_555 D N GLU 267 D GLU 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale15 D C PRO 282 D PRO 282 1_555 D N MSE 283 D MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? covale ? covale16 D C MSE 283 D MSE 283 1_555 D N ARG 284 D ARG 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.283 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 N CA SAM sing 281 n n N HN1 SAM sing 282 n n N HN2 SAM sing 283 n n CA C SAM sing 284 n n CA CB SAM sing 285 n n CA HA SAM sing 286 n n C O SAM doub 287 n n C OXT SAM sing 288 n n CB CG SAM sing 289 n n CB HB1 SAM sing 290 n n CB HB2 SAM sing 291 n n CG SD SAM sing 292 n n CG HG1 SAM sing 293 n n CG HG2 SAM sing 294 n n SD CE SAM sing 295 n n SD C5' SAM sing 296 n n CE HE1 SAM sing 297 n n CE HE2 SAM sing 298 n n CE HE3 SAM sing 299 n n C5' C4' SAM sing 300 n n C5' "H5'1" SAM sing 301 n n C5' "H5'2" SAM sing 302 n n C4' O4' SAM sing 303 n n C4' C3' SAM sing 304 n n C4' H4' SAM sing 305 n n O4' C1' SAM sing 306 n n C3' O3' SAM sing 307 n n C3' C2' SAM sing 308 n n C3' H3' SAM sing 309 n n O3' HO3' SAM sing 310 n n C2' O2' SAM sing 311 n n C2' C1' SAM sing 312 n n C2' H2' SAM sing 313 n n O2' HO2' SAM sing 314 n n C1' N9 SAM sing 315 n n C1' H1' SAM sing 316 n n N9 C8 SAM sing 317 n y N9 C4 SAM sing 318 n y C8 N7 SAM doub 319 n y C8 H8 SAM sing 320 n n N7 C5 SAM sing 321 n y C5 C6 SAM sing 322 n y C5 C4 SAM doub 323 n y C6 N6 SAM sing 324 n n C6 N1 SAM doub 325 n y N6 HN61 SAM sing 326 n n N6 HN62 SAM sing 327 n n N1 C2 SAM sing 328 n y C2 N3 SAM doub 329 n y C2 H2 SAM sing 330 n n N3 C4 SAM sing 331 n y # _atom_sites.entry_id 3VYW _atom_sites.fract_transf_matrix[1][1] 0.018022 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003976 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009295 _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] 0.0087 _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 E 2 SAM A 1 501 501 SAM SAM . F 2 SAM B 1 401 502 SAM SAM . G 3 BEN B 1 402 1001 BEN BEN . H 2 SAM C 1 401 503 SAM SAM . I 3 BEN C 1 402 1002 BEN BEN . J 2 SAM D 1 401 504 SAM SAM . K 4 HOH A 1 601 505 HOH HOH . K 4 HOH A 2 602 506 HOH HOH . K 4 HOH A 3 603 507 HOH HOH . K 4 HOH A 4 604 508 HOH HOH . K 4 HOH A 5 605 509 HOH HOH . K 4 HOH A 6 606 510 HOH HOH . K 4 HOH A 7 607 511 HOH HOH . K 4 HOH A 8 608 512 HOH HOH . K 4 HOH A 9 609 513 HOH HOH . K 4 HOH A 10 610 514 HOH HOH . K 4 HOH A 11 611 515 HOH HOH . K 4 HOH A 12 612 516 HOH HOH . K 4 HOH A 13 613 517 HOH HOH . K 4 HOH A 14 614 518 HOH HOH . K 4 HOH A 15 615 519 HOH HOH . K 4 HOH A 16 616 520 HOH HOH . K 4 HOH A 17 617 521 HOH HOH . K 4 HOH A 18 618 522 HOH HOH . K 4 HOH A 19 619 523 HOH HOH . K 4 HOH A 20 620 524 HOH HOH . K 4 HOH A 21 621 525 HOH HOH . K 4 HOH A 22 622 526 HOH HOH . K 4 HOH A 23 623 527 HOH HOH . K 4 HOH A 24 624 528 HOH HOH . K 4 HOH A 25 625 529 HOH HOH . K 4 HOH A 26 626 530 HOH HOH . K 4 HOH A 27 627 531 HOH HOH . K 4 HOH A 28 628 532 HOH HOH . K 4 HOH A 29 629 533 HOH HOH . K 4 HOH A 30 630 534 HOH HOH . K 4 HOH A 31 631 535 HOH HOH . K 4 HOH A 32 632 536 HOH HOH . K 4 HOH A 33 633 537 HOH HOH . K 4 HOH A 34 634 538 HOH HOH . K 4 HOH A 35 635 539 HOH HOH . K 4 HOH A 36 636 540 HOH HOH . K 4 HOH A 37 637 541 HOH HOH . K 4 HOH A 38 638 542 HOH HOH . K 4 HOH A 39 639 543 HOH HOH . K 4 HOH A 40 640 544 HOH HOH . K 4 HOH A 41 641 545 HOH HOH . K 4 HOH A 42 642 546 HOH HOH . L 4 HOH B 1 501 1003 HOH HOH . L 4 HOH B 2 502 1004 HOH HOH . L 4 HOH B 3 503 1005 HOH HOH . L 4 HOH B 4 504 1006 HOH HOH . L 4 HOH B 5 505 1007 HOH HOH . L 4 HOH B 6 506 1008 HOH HOH . L 4 HOH B 7 507 1009 HOH HOH . L 4 HOH B 8 508 1010 HOH HOH . L 4 HOH B 9 509 1011 HOH HOH . L 4 HOH B 10 510 1012 HOH HOH . L 4 HOH B 11 511 1013 HOH HOH . L 4 HOH B 12 512 1014 HOH HOH . L 4 HOH B 13 513 1015 HOH HOH . L 4 HOH B 14 514 1016 HOH HOH . L 4 HOH B 15 515 1017 HOH HOH . L 4 HOH B 16 516 1018 HOH HOH . L 4 HOH B 17 517 1019 HOH HOH . L 4 HOH B 18 518 1020 HOH HOH . L 4 HOH B 19 519 1021 HOH HOH . L 4 HOH B 20 520 1022 HOH HOH . L 4 HOH B 21 521 1023 HOH HOH . L 4 HOH B 22 522 1024 HOH HOH . L 4 HOH B 23 523 1025 HOH HOH . L 4 HOH B 24 524 1026 HOH HOH . L 4 HOH B 25 525 1027 HOH HOH . L 4 HOH B 26 526 1028 HOH HOH . L 4 HOH B 27 527 1029 HOH HOH . L 4 HOH B 28 528 1030 HOH HOH . L 4 HOH B 29 529 1031 HOH HOH . L 4 HOH B 30 530 1032 HOH HOH . L 4 HOH B 31 531 1033 HOH HOH . L 4 HOH B 32 532 1034 HOH HOH . M 4 HOH C 1 501 1003 HOH HOH . M 4 HOH C 2 502 1004 HOH HOH . M 4 HOH C 3 503 1005 HOH HOH . M 4 HOH C 4 504 1006 HOH HOH . M 4 HOH C 5 505 1007 HOH HOH . M 4 HOH C 6 506 1008 HOH HOH . M 4 HOH C 7 507 1009 HOH HOH . M 4 HOH C 8 508 1010 HOH HOH . M 4 HOH C 9 509 1011 HOH HOH . M 4 HOH C 10 510 1012 HOH HOH . M 4 HOH C 11 511 1013 HOH HOH . M 4 HOH C 12 512 1014 HOH HOH . M 4 HOH C 13 513 1015 HOH HOH . M 4 HOH C 14 514 1016 HOH HOH . M 4 HOH C 15 515 1017 HOH HOH . M 4 HOH C 16 516 1018 HOH HOH . M 4 HOH C 17 517 1019 HOH HOH . M 4 HOH C 18 518 1020 HOH HOH . M 4 HOH C 19 519 1021 HOH HOH . M 4 HOH C 20 520 1022 HOH HOH . M 4 HOH C 21 521 1023 HOH HOH . M 4 HOH C 22 522 1024 HOH HOH . M 4 HOH C 23 523 1025 HOH HOH . M 4 HOH C 24 524 1026 HOH HOH . M 4 HOH C 25 525 1027 HOH HOH . M 4 HOH C 26 526 1028 HOH HOH . M 4 HOH C 27 527 1029 HOH HOH . M 4 HOH C 28 528 1030 HOH HOH . M 4 HOH C 29 529 1031 HOH HOH . M 4 HOH C 30 530 1032 HOH HOH . M 4 HOH C 31 531 1033 HOH HOH . M 4 HOH C 32 532 1034 HOH HOH . M 4 HOH C 33 533 1035 HOH HOH . M 4 HOH C 34 534 1036 HOH HOH . N 4 HOH D 1 501 505 HOH HOH . N 4 HOH D 2 502 506 HOH HOH . N 4 HOH D 3 503 507 HOH HOH . N 4 HOH D 4 504 508 HOH HOH . N 4 HOH D 5 505 509 HOH HOH . N 4 HOH D 6 506 510 HOH HOH . N 4 HOH D 7 507 511 HOH HOH . N 4 HOH D 8 508 512 HOH HOH . N 4 HOH D 9 509 513 HOH HOH . N 4 HOH D 10 510 514 HOH HOH . N 4 HOH D 11 511 515 HOH HOH . N 4 HOH D 12 512 516 HOH HOH . N 4 HOH D 13 513 517 HOH HOH . N 4 HOH D 14 514 518 HOH HOH . N 4 HOH D 15 515 519 HOH HOH . N 4 HOH D 16 516 520 HOH HOH . N 4 HOH D 17 517 521 HOH HOH . N 4 HOH D 18 518 522 HOH HOH . N 4 HOH D 19 519 523 HOH HOH . N 4 HOH D 20 520 524 HOH HOH . N 4 HOH D 21 521 525 HOH HOH . N 4 HOH D 22 522 526 HOH HOH . N 4 HOH D 23 523 527 HOH HOH . N 4 HOH D 24 524 528 HOH HOH . N 4 HOH D 25 525 529 HOH HOH . N 4 HOH D 26 526 530 HOH HOH . N 4 HOH D 27 527 531 HOH HOH . N 4 HOH D 28 528 532 HOH HOH . N 4 HOH D 29 529 533 HOH HOH . N 4 HOH D 30 530 534 HOH HOH . N 4 HOH D 31 531 535 HOH HOH . N 4 HOH D 32 532 536 HOH HOH . N 4 HOH D 33 533 537 HOH HOH . N 4 HOH D 34 534 538 HOH HOH . N 4 HOH D 35 535 539 HOH HOH . N 4 HOH D 36 536 540 HOH HOH . N 4 HOH D 37 537 541 HOH HOH . N 4 HOH D 38 538 542 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 N N SAM . . . J 2 56.831 -19.852 -41.54 1 52.27 ? N SAM 401 D 1 HETATM 2 C CA SAM . . . J 2 57.05 -18.641 -40.817 1 63.96 ? CA SAM 401 D 1 HETATM 3 C C SAM . . . J 2 56.626 -18.846 -39.411 1 65.23 ? C SAM 401 D 1 HETATM 4 O O SAM . . . J 2 56.726 -17.961 -38.57 1 62.74 ? O SAM 401 D 1 HETATM 5 O OXT SAM . . . J 2 56.226 -19.95 -39.121 1 66.26 ? OXT SAM 401 D 1 HETATM 6 C CB SAM . . . J 2 56.355 -17.515 -41.547 1 65.7 ? CB SAM 401 D 1 HETATM 7 C CG SAM . . . J 2 57.266 -17.104 -42.694 1 63.96 ? CG SAM 401 D 1 HETATM 8 S SD SAM . . . J 2 57.043 -15.572 -43.21 1 59.81 ? SD SAM 401 D 1 HETATM 9 C CE SAM . . . J 2 55.54 -15.48 -43.816 1 55.74 ? CE SAM 401 D 1 HETATM 10 C C5' SAM . . . J 2 58.035 -15.271 -44.509 1 60.69 ? C5' SAM 401 D 1 HETATM 11 C C4' SAM . . . J 2 59.545 -15.46 -44.309 1 57.02 ? C4' SAM 401 D 1 HETATM 12 O O4' SAM . . . J 2 60.186 -15.717 -45.546 1 54.57 ? O4' SAM 401 D 1 HETATM 13 C C3' SAM . . . J 2 60.255 -14.255 -43.756 1 50.54 ? C3' SAM 401 D 1 HETATM 14 O O3' SAM . . . J 2 61.087 -14.704 -42.705 1 50.29 ? O3' SAM 401 D 1 HETATM 15 C C2' SAM . . . J 2 61.078 -13.757 -44.914 1 48.66 ? C2' SAM 401 D 1 HETATM 16 O O2' SAM . . . J 2 62.258 -13.033 -44.609 1 41.87 ? O2' SAM 401 D 1 HETATM 17 C C1' SAM . . . J 2 61.418 -15.034 -45.582 1 48.99 ? C1' SAM 401 D 1 HETATM 18 N N9 SAM . . . J 2 61.87 -14.759 -46.945 1 52.88 ? N9 SAM 401 D 1 HETATM 19 C C8 SAM . . . J 2 61.313 -13.919 -47.787 1 49.97 ? C8 SAM 401 D 1 HETATM 20 N N7 SAM . . . J 2 61.967 -13.903 -48.93 1 50.07 ? N7 SAM 401 D 1 HETATM 21 C C5 SAM . . . J 2 62.964 -14.743 -48.842 1 46.64 ? C5 SAM 401 D 1 HETATM 22 C C6 SAM . . . J 2 64.04 -15.21 -49.711 1 46.18 ? C6 SAM 401 D 1 HETATM 23 N N6 SAM . . . J 2 64.202 -14.742 -50.949 1 37.16 ? N6 SAM 401 D 1 HETATM 24 N N1 SAM . . . J 2 64.871 -16.099 -49.202 1 48.22 ? N1 SAM 401 D 1 HETATM 25 C C2 SAM . . . J 2 64.748 -16.562 -47.98 1 47.72 ? C2 SAM 401 D 1 HETATM 26 N N3 SAM . . . J 2 63.801 -16.191 -47.157 1 51.81 ? N3 SAM 401 D 1 HETATM 27 C C4 SAM . . . J 2 62.902 -15.297 -47.524 1 49.81 ? C4 SAM 401 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #