data_4NAK # _model_server_result.job_id P1Gz_M8sp9MZZUVILuj7ew _model_server_result.datetime_utc '2024-12-29 09:38:27' _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 4nak # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4NAK # _exptl.entry_id 4NAK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 154.251 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DIHYDROXY-1,4-DITHIOBUTANE _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 4NAK _cell.length_a 75.24 _cell.length_b 75.24 _cell.length_c 224.14 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NAK _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,F,G,H,I,J,K,L,M,N,O _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' 17_554 x-y+1/3,-y+2/3,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 43.439834 -74.713333 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A O ILE 34 A ILE 108 1_555 L K K . A K 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc2 A O ALA 35 A ALA 109 1_555 L K K . A K 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.493 ? metalc ? metalc3 A OG SER 38 A SER 112 1_555 L K K . A K 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc4 A O SER 43 A SER 117 1_555 M K K . A K 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? metalc ? metalc5 A O MET 45 A MET 119 1_555 M K K . A K 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc6 A O VAL 48 A VAL 122 1_555 M K K . A K 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.35 ? metalc ? metalc7 A OE2 GLU 64 A GLU 138 1_555 G CD CD . A CD 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc8 A OE1 GLU 67 A GLU 141 1_555 G CD CD . A CD 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc9 A O ASP 71 A ASP 145 1_555 M K K . A K 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.429 ? metalc ? metalc10 A OE1 GLU 93 A GLU 167 1_555 E CD CD . A CD 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc11 A OE2 GLU 93 A GLU 167 1_555 E CD CD . A CD 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc12 A O SER 106 A SER 180 1_555 L K K . A K 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc13 A OD2 ASP 115 A ASP 189 1_555 N K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc14 A OE1 GLN 164 A GLN 238 1_555 D CD CD . A CD 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc15 A OD1 ASP 187 A ASP 261 1_555 F CD CD . A CD 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc16 A ND1 HIS 197 A HIS 271 1_555 H CD CD . A CD 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc17 A OD1 ASN 208 A ASN 282 1_555 K K K . A K 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc18 A O ILE 209 A ILE 283 1_555 K K K . A K 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc19 A OD2 ASP 216 A ASP 290 1_555 I K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc20 A OD1 ASP 216 A ASP 290 1_555 I K K . A K 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.296 ? metalc ? metalc21 B N11 PBQ . A PBQ 401 1_555 D CD CD . A CD 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc22 B O PBQ . A PBQ 401 1_555 D CD CD . A CD 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc23 F CD CD . A CD 405 1_555 O O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc24 F CD CD . A CD 405 1_555 O O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc25 H CD CD . A CD 407 1_555 O O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc26 J K K . A K 409 1_555 O O HOH . A HOH 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.239 ? metalc ? metalc27 N K K . A K 413 1_555 O O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc28 N K K . A K 413 1_555 O O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? # _chem_comp.formula 'C4 H10 O2 S2' _chem_comp.formula_weight 154.251 _chem_comp.id DTT _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DIHYDROXY-1,4-DITHIOBUTANE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,4-DITHIOTHREITOL # 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 S1 C1 DTT sing 83 n n S1 HS1 DTT sing 84 n n C1 C2 DTT sing 85 n n C1 H11 DTT sing 86 n n C1 H12 DTT sing 87 n n C2 O2 DTT sing 88 n n C2 C3 DTT sing 89 n n C2 H2 DTT sing 90 n n O2 HO2 DTT sing 91 n n C3 O3 DTT sing 92 n n C3 C4 DTT sing 93 n n C3 H3 DTT sing 94 n n O3 HO3 DTT sing 95 n n C4 S4 DTT sing 96 n n C4 H41 DTT sing 97 n n C4 H42 DTT sing 98 n n S4 HS2 DTT sing 99 n n # _atom_sites.entry_id 4NAK _atom_sites.fract_transf_matrix[1][1] 0.013291 _atom_sites.fract_transf_matrix[1][2] 0.007673 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015347 _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] 0.004461 _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 PBQ A 1 401 1 PBQ LIG . C 3 DTT A 1 402 1 DTT DTT . D 4 CD A 1 403 1 CD CD . E 4 CD A 1 404 404 CD CD . F 4 CD A 1 405 3 CD CD . G 4 CD A 1 406 4 CD CD . H 4 CD A 1 407 5 CD CD . I 5 K A 1 408 6 K K . J 5 K A 1 409 7 K K . K 5 K A 1 410 8 K K . L 5 K A 1 411 19 K K . M 5 K A 1 412 10 K K . N 5 K A 1 413 11 K K . O 6 HOH A 1 501 12 HOH HOH . O 6 HOH A 2 502 13 HOH HOH . O 6 HOH A 3 503 15 HOH HOH . O 6 HOH A 4 504 16 HOH HOH . O 6 HOH A 5 505 19 HOH HOH . O 6 HOH A 6 506 20 HOH HOH . O 6 HOH A 7 507 22 HOH HOH . O 6 HOH A 8 508 23 HOH HOH . O 6 HOH A 9 509 24 HOH HOH . O 6 HOH A 10 510 25 HOH HOH . O 6 HOH A 11 511 26 HOH HOH . O 6 HOH A 12 512 27 HOH HOH . O 6 HOH A 13 513 28 HOH HOH . O 6 HOH A 14 514 29 HOH HOH . O 6 HOH A 15 515 30 HOH HOH . O 6 HOH A 16 516 31 HOH HOH . O 6 HOH A 17 517 32 HOH HOH . O 6 HOH A 18 518 33 HOH HOH . O 6 HOH A 19 519 34 HOH HOH . O 6 HOH A 20 520 37 HOH HOH . O 6 HOH A 21 521 38 HOH HOH . O 6 HOH A 22 522 39 HOH HOH . O 6 HOH A 23 523 40 HOH HOH . O 6 HOH A 24 524 41 HOH HOH . O 6 HOH A 25 525 42 HOH HOH . O 6 HOH A 26 526 43 HOH HOH . O 6 HOH A 27 527 44 HOH HOH . O 6 HOH A 28 528 45 HOH HOH . O 6 HOH A 29 529 46 HOH HOH . O 6 HOH A 30 530 48 HOH HOH . O 6 HOH A 31 531 49 HOH HOH . O 6 HOH A 32 532 51 HOH HOH . O 6 HOH A 33 533 52 HOH HOH . O 6 HOH A 34 534 53 HOH HOH . O 6 HOH A 35 535 54 HOH HOH . O 6 HOH A 36 536 56 HOH HOH . O 6 HOH A 37 537 57 HOH HOH . O 6 HOH A 38 538 58 HOH HOH . O 6 HOH A 39 539 61 HOH HOH . O 6 HOH A 40 540 62 HOH HOH . O 6 HOH A 41 541 63 HOH HOH . O 6 HOH A 42 542 64 HOH HOH . O 6 HOH A 43 543 65 HOH HOH . O 6 HOH A 44 544 66 HOH HOH . O 6 HOH A 45 545 67 HOH HOH . O 6 HOH A 46 546 68 HOH HOH . O 6 HOH A 47 547 69 HOH HOH . O 6 HOH A 48 548 70 HOH HOH . O 6 HOH A 49 549 71 HOH HOH . O 6 HOH A 50 550 72 HOH HOH . O 6 HOH A 51 551 73 HOH HOH . O 6 HOH A 52 552 74 HOH HOH . O 6 HOH A 53 553 75 HOH HOH . O 6 HOH A 54 554 76 HOH HOH . O 6 HOH A 55 555 77 HOH HOH . O 6 HOH A 56 556 78 HOH HOH . O 6 HOH A 57 557 79 HOH HOH . O 6 HOH A 58 558 80 HOH HOH . O 6 HOH A 59 559 81 HOH HOH . O 6 HOH A 60 560 82 HOH HOH . O 6 HOH A 61 561 83 HOH HOH . O 6 HOH A 62 562 85 HOH HOH . O 6 HOH A 63 563 86 HOH HOH . O 6 HOH A 64 564 87 HOH HOH . O 6 HOH A 65 565 90 HOH HOH . O 6 HOH A 66 566 92 HOH HOH . O 6 HOH A 67 567 93 HOH HOH . O 6 HOH A 68 568 94 HOH HOH . O 6 HOH A 69 569 96 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 S S1 DTT . . . C 3 2.584 43.108 -21.895 1 52.35 ? S1 DTT 402 A 1 HETATM 2 C C1 DTT . . . C 3 3.597 43.912 -23.182 1 46.91 ? C1 DTT 402 A 1 HETATM 3 C C2 DTT . . . C 3 2.865 44.004 -24.519 1 60.47 ? C2 DTT 402 A 1 HETATM 4 O O2 DTT . . . C 3 3.639 43.337 -25.523 1 68.75 ? O2 DTT 402 A 1 HETATM 5 C C3 DTT . . . C 3 2.57 45.429 -24.991 1 62.99 ? C3 DTT 402 A 1 HETATM 6 O O3 DTT . . . C 3 1.18 45.544 -25.321 1 65.42 ? O3 DTT 402 A 1 HETATM 7 C C4 DTT . . . C 3 2.962 46.511 -23.986 1 60.03 ? C4 DTT 402 A 1 HETATM 8 S S4 DTT . . . C 3 1.691 46.863 -22.753 1 53.69 ? S4 DTT 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #