data_3DCM # _model_server_result.job_id TlABMvhtvGc1tKR2fAeyLQ _model_server_result.datetime_utc '2025-03-04 22:07:15' _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 3dcm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":5452}' # _entry.id 3DCM # _exptl.entry_id 3DCM _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 129.03 _cell.angle_gamma 90 _cell.entry_id 3DCM _cell.length_a 79.648 _cell.length_b 63.402 _cell.length_c 54.522 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DCM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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 _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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 45.314013 0 42.353581 # _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 # _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 264 n n N HN1 SAM sing 265 n n N HN2 SAM sing 266 n n CA C SAM sing 267 n n CA CB SAM sing 268 n n CA HA SAM sing 269 n n C O SAM doub 270 n n C OXT SAM sing 271 n n CB CG SAM sing 272 n n CB HB1 SAM sing 273 n n CB HB2 SAM sing 274 n n CG SD SAM sing 275 n n CG HG1 SAM sing 276 n n CG HG2 SAM sing 277 n n SD CE SAM sing 278 n n SD C5' SAM sing 279 n n CE HE1 SAM sing 280 n n CE HE2 SAM sing 281 n n CE HE3 SAM sing 282 n n C5' C4' SAM sing 283 n n C5' "H5'1" SAM sing 284 n n C5' "H5'2" SAM sing 285 n n C4' O4' SAM sing 286 n n C4' C3' SAM sing 287 n n C4' H4' SAM sing 288 n n O4' C1' SAM sing 289 n n C3' O3' SAM sing 290 n n C3' C2' SAM sing 291 n n C3' H3' SAM sing 292 n n O3' HO3' SAM sing 293 n n C2' O2' SAM sing 294 n n C2' C1' SAM sing 295 n n C2' H2' SAM sing 296 n n O2' HO2' SAM sing 297 n n C1' N9 SAM sing 298 n n C1' H1' SAM sing 299 n n N9 C8 SAM sing 300 n y N9 C4 SAM sing 301 n y C8 N7 SAM doub 302 n y C8 H8 SAM sing 303 n n N7 C5 SAM sing 304 n y C5 C6 SAM sing 305 n y C5 C4 SAM doub 306 n y C6 N6 SAM sing 307 n n C6 N1 SAM doub 308 n y N6 HN61 SAM sing 309 n n N6 HN62 SAM sing 310 n n N1 C2 SAM sing 311 n y C2 N3 SAM doub 312 n y C2 H2 SAM sing 313 n n N3 C4 SAM sing 314 n y # _atom_sites.entry_id 3DCM _atom_sites.fract_transf_matrix[1][1] 0.012555 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.010178 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015772 _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] 0.023611 _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 SAM X 1 5452 5452 SAM SAM . C 3 HOH X 1 5453 1 HOH HOH . C 3 HOH X 2 5454 2 HOH HOH . C 3 HOH X 3 5455 3 HOH HOH . C 3 HOH X 4 5456 4 HOH HOH . C 3 HOH X 5 5457 5 HOH HOH . C 3 HOH X 6 5458 6 HOH HOH . C 3 HOH X 7 5459 7 HOH HOH . C 3 HOH X 8 5460 8 HOH HOH . C 3 HOH X 9 5461 9 HOH HOH . C 3 HOH X 10 5462 10 HOH HOH . C 3 HOH X 11 5463 11 HOH HOH . C 3 HOH X 12 5464 12 HOH HOH . C 3 HOH X 13 5465 13 HOH HOH . C 3 HOH X 14 5466 14 HOH HOH . C 3 HOH X 15 5467 15 HOH HOH . C 3 HOH X 16 5468 16 HOH HOH . C 3 HOH X 17 5469 17 HOH HOH . C 3 HOH X 18 5470 18 HOH HOH . C 3 HOH X 19 5471 19 HOH HOH . C 3 HOH X 20 5472 20 HOH HOH . C 3 HOH X 21 5473 21 HOH HOH . C 3 HOH X 22 5474 22 HOH HOH . C 3 HOH X 23 5475 23 HOH HOH . C 3 HOH X 24 5476 24 HOH HOH . C 3 HOH X 25 5477 25 HOH HOH . C 3 HOH X 26 5478 26 HOH HOH . C 3 HOH X 27 5479 27 HOH HOH . C 3 HOH X 28 5480 28 HOH HOH . C 3 HOH X 29 5481 29 HOH HOH . C 3 HOH X 30 5482 30 HOH HOH . C 3 HOH X 31 5483 31 HOH HOH . C 3 HOH X 32 5484 32 HOH HOH . C 3 HOH X 33 5485 33 HOH HOH . C 3 HOH X 34 5486 34 HOH HOH . C 3 HOH X 35 5487 35 HOH HOH . C 3 HOH X 36 5488 36 HOH HOH . C 3 HOH X 37 5489 37 HOH HOH . C 3 HOH X 38 5490 38 HOH HOH . C 3 HOH X 39 5491 39 HOH HOH . C 3 HOH X 40 5492 40 HOH HOH . C 3 HOH X 41 5493 41 HOH HOH . C 3 HOH X 42 5494 42 HOH HOH . C 3 HOH X 43 5495 43 HOH HOH . C 3 HOH X 44 5496 44 HOH HOH . C 3 HOH X 45 5497 45 HOH HOH . C 3 HOH X 46 5498 46 HOH HOH . C 3 HOH X 47 5499 47 HOH HOH . C 3 HOH X 48 5500 48 HOH HOH . C 3 HOH X 49 5501 49 HOH HOH . C 3 HOH X 50 5502 50 HOH HOH . C 3 HOH X 51 5503 51 HOH HOH . C 3 HOH X 52 5504 52 HOH HOH . C 3 HOH X 53 5505 53 HOH HOH . C 3 HOH X 54 5506 54 HOH HOH . C 3 HOH X 55 5507 55 HOH HOH . C 3 HOH X 56 5508 56 HOH HOH . C 3 HOH X 57 5509 57 HOH HOH . C 3 HOH X 58 5510 58 HOH HOH . C 3 HOH X 59 5511 59 HOH HOH . C 3 HOH X 60 5512 60 HOH HOH . C 3 HOH X 61 5513 61 HOH HOH . C 3 HOH X 62 5514 62 HOH HOH . C 3 HOH X 63 5515 63 HOH HOH . C 3 HOH X 64 5516 64 HOH HOH . C 3 HOH X 65 5517 65 HOH HOH . C 3 HOH X 66 5518 66 HOH HOH . C 3 HOH X 67 5519 67 HOH HOH . C 3 HOH X 68 5520 68 HOH HOH . C 3 HOH X 69 5521 69 HOH HOH . C 3 HOH X 70 5522 70 HOH HOH . C 3 HOH X 71 5523 71 HOH HOH . C 3 HOH X 72 5524 72 HOH HOH . C 3 HOH X 73 5525 73 HOH HOH . C 3 HOH X 74 5526 74 HOH HOH . C 3 HOH X 75 5527 75 HOH HOH . C 3 HOH X 76 5528 76 HOH HOH . C 3 HOH X 77 5529 77 HOH HOH . C 3 HOH X 78 5530 78 HOH HOH . C 3 HOH X 79 5531 2 HOH HOH . C 3 HOH X 80 5532 7 HOH HOH . C 3 HOH X 81 5533 8 HOH HOH . C 3 HOH X 82 5534 9 HOH HOH . C 3 HOH X 83 5535 10 HOH HOH . C 3 HOH X 84 5536 11 HOH HOH . C 3 HOH X 85 5537 13 HOH HOH . C 3 HOH X 86 5538 14 HOH HOH . C 3 HOH X 87 5539 15 HOH HOH . C 3 HOH X 88 5540 19 HOH HOH . C 3 HOH X 89 5541 21 HOH HOH . C 3 HOH X 90 5542 25 HOH HOH . C 3 HOH X 91 5543 27 HOH HOH . C 3 HOH X 92 5544 30 HOH HOH . C 3 HOH X 93 5545 31 HOH HOH . C 3 HOH X 94 5546 32 HOH HOH . C 3 HOH X 95 5547 33 HOH HOH . C 3 HOH X 96 5548 38 HOH HOH . C 3 HOH X 97 5549 39 HOH HOH . C 3 HOH X 98 5550 43 HOH HOH . C 3 HOH X 99 5551 44 HOH HOH . C 3 HOH X 100 5552 47 HOH HOH . C 3 HOH X 101 5553 49 HOH HOH . C 3 HOH X 102 5554 53 HOH HOH . C 3 HOH X 103 5555 55 HOH HOH . C 3 HOH X 104 5556 57 HOH HOH . C 3 HOH X 105 5557 60 HOH HOH . C 3 HOH X 106 5558 68 HOH HOH . C 3 HOH X 107 5559 69 HOH HOH . C 3 HOH X 108 5560 70 HOH HOH . C 3 HOH X 109 5561 85 HOH HOH . C 3 HOH X 110 5562 86 HOH HOH . C 3 HOH X 111 5563 96 HOH HOH . C 3 HOH X 112 5564 100 HOH HOH . C 3 HOH X 113 5565 102 HOH HOH . C 3 HOH X 114 5566 103 HOH HOH . C 3 HOH X 115 5567 104 HOH HOH . C 3 HOH X 116 5568 105 HOH HOH . C 3 HOH X 117 5569 107 HOH HOH . C 3 HOH X 118 5570 111 HOH HOH . C 3 HOH X 119 5571 112 HOH HOH . C 3 HOH X 120 5572 113 HOH HOH . C 3 HOH X 121 5573 115 HOH HOH . C 3 HOH X 122 5574 17 HOH HOH . C 3 HOH X 123 5575 25 HOH HOH . C 3 HOH X 124 5576 27 HOH HOH . C 3 HOH X 125 5577 30 HOH HOH . C 3 HOH X 126 5578 60 HOH HOH . C 3 HOH X 127 5579 81 HOH HOH . C 3 HOH X 128 5580 89 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 . . . B 2 13.639 38.674 15.757 1 35.11 ? N SAM 5452 X 1 HETATM 2 C CA SAM . . . B 2 14.456 37.496 16.062 1 34.81 ? CA SAM 5452 X 1 HETATM 3 C C SAM . . . B 2 15.901 37.895 16.39 1 35.26 ? C SAM 5452 X 1 HETATM 4 O O SAM . . . B 2 16.097 38.864 17.131 1 35.83 ? O SAM 5452 X 1 HETATM 5 O OXT SAM . . . B 2 16.896 37.288 15.956 1 34.87 ? OXT SAM 5452 X 1 HETATM 6 C CB SAM . . . B 2 14.35 36.436 14.957 1 34.47 ? CB SAM 5452 X 1 HETATM 7 C CG SAM . . . B 2 14.543 36.927 13.52 1 31.87 ? CG SAM 5452 X 1 HETATM 8 S SD SAM . . . B 2 14.798 35.631 12.267 1 28.42 ? SD SAM 5452 X 1 HETATM 9 C CE SAM . . . B 2 13.085 35.152 11.912 1 27.23 ? CE SAM 5452 X 1 HETATM 10 C C5' SAM . . . B 2 15.364 34.207 13.227 1 23.42 ? C5' SAM 5452 X 1 HETATM 11 C C4' SAM . . . B 2 16.273 33.311 12.394 1 20.05 ? C4' SAM 5452 X 1 HETATM 12 O O4' SAM . . . B 2 16.908 32.384 13.246 1 19 ? O4' SAM 5452 X 1 HETATM 13 C C3' SAM . . . B 2 15.506 32.479 11.377 1 18.07 ? C3' SAM 5452 X 1 HETATM 14 O O3' SAM . . . B 2 15.494 33.071 10.107 1 17.43 ? O3' SAM 5452 X 1 HETATM 15 C C2' SAM . . . B 2 16.216 31.138 11.368 1 17.66 ? C2' SAM 5452 X 1 HETATM 16 O O2' SAM . . . B 2 17.348 31.14 10.524 1 15.46 ? O2' SAM 5452 X 1 HETATM 17 C C1' SAM . . . B 2 16.709 31.055 12.789 1 16.74 ? C1' SAM 5452 X 1 HETATM 18 N N9 SAM . . . B 2 15.747 30.374 13.684 1 15.81 ? N9 SAM 5452 X 1 HETATM 19 C C8 SAM . . . B 2 14.99 30.946 14.673 1 14.76 ? C8 SAM 5452 X 1 HETATM 20 N N7 SAM . . . B 2 14.273 29.975 15.283 1 15.27 ? N7 SAM 5452 X 1 HETATM 21 C C5 SAM . . . B 2 14.574 28.794 14.698 1 15.63 ? C5 SAM 5452 X 1 HETATM 22 C C6 SAM . . . B 2 14.138 27.495 14.924 1 16.25 ? C6 SAM 5452 X 1 HETATM 23 N N6 SAM . . . B 2 13.246 27.229 15.878 1 14.93 ? N6 SAM 5452 X 1 HETATM 24 N N1 SAM . . . B 2 14.653 26.472 14.153 1 16.71 ? N1 SAM 5452 X 1 HETATM 25 C C2 SAM . . . B 2 15.573 26.725 13.158 1 16.06 ? C2 SAM 5452 X 1 HETATM 26 N N3 SAM . . . B 2 15.998 28.019 12.934 1 15.53 ? N3 SAM 5452 X 1 HETATM 27 C C4 SAM . . . B 2 15.503 29.03 13.698 1 15.95 ? C4 SAM 5452 X 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #