data_5M25 # _model_server_result.job_id aSklya59P2jCIu_APp2Uew _model_server_result.datetime_utc '2024-11-21 18:00:37' _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 5m25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5M25 # _exptl.entry_id 5M25 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 626.707 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-~{N}-[(2~{S})-1-[[4-[(~{E})-[4-(hydroxymethyl)phenyl]diazenyl]phenyl]methylamino]-1-oxidanylidene-propan-2-yl]pentanamide _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 90 _cell.entry_id 5M25 _cell.length_a 80.714 _cell.length_b 85.917 _cell.length_c 39.276 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M25 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _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 'C29 H42 N10 O6' _chem_comp.formula_weight 626.707 _chem_comp.id 7DU _chem_comp.mon_nstd_flag . _chem_comp.name (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-~{N}-[(2~{S})-1-[[4-[(~{E})-[4-(hydroxymethyl)phenyl]diazenyl]phenyl]methylamino]-1-oxidanylidene-propan-2-yl]pentanamide _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 NAS CAU 7DU doub 1 n n CAU NAT 7DU sing 2 n n CAU NAV 7DU sing 3 n n NAV CAQ 7DU sing 4 n n CAQ CAR 7DU sing 5 n n CAR CAW 7DU sing 6 n n CAW CAM 7DU sing 7 n n OG CB 7DU sing 8 n n CB CA 7DU sing 9 n n CAM NAO 7DU sing 10 n n CAM CAN 7DU sing 11 n n NAO CAJ 7DU sing 12 n n CA N 7DU sing 13 n n CA C 7DU sing 14 n n CAN NBA 7DU sing 15 n n CAN OAP 7DU doub 16 n n NBA CAY 7DU sing 17 n n CAX CAY 7DU sing 18 n n CAY CAZ 7DU sing 19 n n C NAK 7DU sing 20 n n C O 7DU doub 21 n n NAK CAI 7DU sing 22 n n CAJ CAI 7DU sing 23 n n CAJ OAL 7DU doub 24 n n CAH CAI 7DU sing 25 n n CAZ OBB 7DU doub 26 n n CAZ NDB 7DU sing 27 n n NDB CDC 7DU sing 28 n n CDI CDH 7DU doub 29 n y CDI CDD 7DU sing 30 n y CDH CDG 7DU sing 31 n y CDC CDD 7DU sing 32 n n CDD CDE 7DU doub 33 n y CDG NDJ 7DU sing 34 n n CDG CDF 7DU doub 35 n y NDJ NDK 7DU doub 36 n n CDE CDF 7DU sing 37 n y CDM CDN 7DU doub 38 n y CDM CDL 7DU sing 39 n y CDN CDO 7DU sing 40 n y NDK CDL 7DU sing 41 n n CDL CDQ 7DU doub 42 n y ODS CDR 7DU sing 43 n n CDO CDR 7DU sing 44 n n CDO CDP 7DU doub 45 n y CDQ CDP 7DU sing 46 n y CDH H1 7DU sing 47 n n CDI H2 7DU sing 48 n n CDF H3 7DU sing 49 n n CDE H4 7DU sing 50 n n CDC H5 7DU sing 51 n n CDC H6 7DU sing 52 n n NDB H7 7DU sing 53 n n CAY H8 7DU sing 54 n n CAX H9 7DU sing 55 n n CAX H10 7DU sing 56 n n CAX H11 7DU sing 57 n n NBA H12 7DU sing 58 n n CAM H13 7DU sing 59 n n CAW H14 7DU sing 60 n n CAW H15 7DU sing 61 n n CAR H16 7DU sing 62 n n CAR H17 7DU sing 63 n n CAQ H18 7DU sing 64 n n CAQ H19 7DU sing 65 n n NAV H20 7DU sing 66 n n NAT H21 7DU sing 67 n n NAT H22 7DU sing 68 n n NAS H23 7DU sing 69 n n NAO H25 7DU sing 70 n n CAI H26 7DU sing 71 n n CAH H27 7DU sing 72 n n CAH H28 7DU sing 73 n n CAH H29 7DU sing 74 n n NAK H30 7DU sing 75 n n CA H31 7DU sing 76 n n N H32 7DU sing 77 n n N H33 7DU sing 78 n n CB H35 7DU sing 79 n n CB H36 7DU sing 80 n n OG H37 7DU sing 81 n n CDR H38 7DU sing 82 n n CDR H39 7DU sing 83 n n ODS H40 7DU sing 84 n n CDP H41 7DU sing 85 n n CDQ H42 7DU sing 86 n n CDN H43 7DU sing 87 n n CDM H44 7DU sing 88 n n # _atom_sites.entry_id 5M25 _atom_sites.fract_transf_matrix[1][1] 0.012389 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011639 _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] 0.025461 _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 7DU A 1 401 333 7DU DJC . C 3 HOH A 1 501 31 HOH HOH . C 3 HOH A 2 502 25 HOH HOH . C 3 HOH A 3 503 20 HOH HOH . C 3 HOH A 4 504 55 HOH HOH . C 3 HOH A 5 505 35 HOH HOH . C 3 HOH A 6 506 84 HOH HOH . C 3 HOH A 7 507 37 HOH HOH . C 3 HOH A 8 508 23 HOH HOH . C 3 HOH A 9 509 32 HOH HOH . C 3 HOH A 10 510 15 HOH HOH . C 3 HOH A 11 511 7 HOH HOH . C 3 HOH A 12 512 8 HOH HOH . C 3 HOH A 13 513 2 HOH HOH . C 3 HOH A 14 514 54 HOH HOH . C 3 HOH A 15 515 38 HOH HOH . C 3 HOH A 16 516 58 HOH HOH . C 3 HOH A 17 517 44 HOH HOH . C 3 HOH A 18 518 34 HOH HOH . C 3 HOH A 19 519 30 HOH HOH . C 3 HOH A 20 520 57 HOH HOH . C 3 HOH A 21 521 9 HOH HOH . C 3 HOH A 22 522 12 HOH HOH . C 3 HOH A 23 523 60 HOH HOH . C 3 HOH A 24 524 27 HOH HOH . C 3 HOH A 25 525 16 HOH HOH . C 3 HOH A 26 526 33 HOH HOH . C 3 HOH A 27 527 49 HOH HOH . C 3 HOH A 28 528 71 HOH HOH . C 3 HOH A 29 529 63 HOH HOH . C 3 HOH A 30 530 3 HOH HOH . C 3 HOH A 31 531 28 HOH HOH . C 3 HOH A 32 532 6 HOH HOH . C 3 HOH A 33 533 92 HOH HOH . C 3 HOH A 34 534 11 HOH HOH . C 3 HOH A 35 535 76 HOH HOH . C 3 HOH A 36 536 64 HOH HOH . C 3 HOH A 37 537 52 HOH HOH . C 3 HOH A 38 538 39 HOH HOH . C 3 HOH A 39 539 1 HOH HOH . C 3 HOH A 40 540 83 HOH HOH . C 3 HOH A 41 541 40 HOH HOH . C 3 HOH A 42 542 14 HOH HOH . C 3 HOH A 43 543 22 HOH HOH . C 3 HOH A 44 544 10 HOH HOH . C 3 HOH A 45 545 85 HOH HOH . C 3 HOH A 46 546 26 HOH HOH . C 3 HOH A 47 547 19 HOH HOH . C 3 HOH A 48 548 24 HOH HOH . C 3 HOH A 49 549 53 HOH HOH . C 3 HOH A 50 550 90 HOH HOH . C 3 HOH A 51 551 45 HOH HOH . C 3 HOH A 52 552 17 HOH HOH . C 3 HOH A 53 553 47 HOH HOH . C 3 HOH A 54 554 77 HOH HOH . C 3 HOH A 55 555 62 HOH HOH . C 3 HOH A 56 556 36 HOH HOH . C 3 HOH A 57 557 66 HOH HOH . C 3 HOH A 58 558 13 HOH HOH . C 3 HOH A 59 559 56 HOH HOH . C 3 HOH A 60 560 50 HOH HOH . C 3 HOH A 61 561 89 HOH HOH . C 3 HOH A 62 562 61 HOH HOH . C 3 HOH A 63 563 87 HOH HOH . C 3 HOH A 64 564 65 HOH HOH . C 3 HOH A 65 565 51 HOH HOH . C 3 HOH A 66 566 48 HOH HOH . C 3 HOH A 67 567 5 HOH HOH . C 3 HOH A 68 568 43 HOH HOH . C 3 HOH A 69 569 42 HOH HOH . C 3 HOH A 70 570 69 HOH HOH . C 3 HOH A 71 571 68 HOH HOH . C 3 HOH A 72 572 70 HOH HOH . C 3 HOH A 73 573 67 HOH HOH . C 3 HOH A 74 574 79 HOH HOH . C 3 HOH A 75 575 72 HOH HOH . C 3 HOH A 76 576 29 HOH HOH . C 3 HOH A 77 577 4 HOH HOH . C 3 HOH A 78 578 41 HOH HOH . C 3 HOH A 79 579 18 HOH HOH . C 3 HOH A 80 580 97 HOH HOH . C 3 HOH A 81 581 80 HOH HOH . C 3 HOH A 82 582 81 HOH HOH . C 3 HOH A 83 583 59 HOH HOH . C 3 HOH A 84 584 93 HOH HOH . C 3 HOH A 85 585 95 HOH HOH . C 3 HOH A 86 586 98 HOH HOH . C 3 HOH A 87 587 78 HOH HOH . C 3 HOH A 88 588 46 HOH HOH . C 3 HOH A 89 589 82 HOH HOH . C 3 HOH A 90 590 88 HOH HOH . C 3 HOH A 91 591 21 HOH HOH . C 3 HOH A 92 592 94 HOH HOH . C 3 HOH A 93 593 96 HOH HOH . C 3 HOH A 94 594 91 HOH HOH . C 3 HOH A 95 595 75 HOH HOH . C 3 HOH A 96 596 74 HOH HOH . C 3 HOH A 97 597 73 HOH HOH . C 3 HOH A 98 598 86 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 NDJ 7DU . . . B 2 -12.535 22.348 8.176 1 31.88 ? NDJ 7DU 401 A 1 HETATM 2 C CDG 7DU . . . B 2 -11.517 23.336 7.95 1 28.54 ? CDG 7DU 401 A 1 HETATM 3 C CDH 7DU . . . B 2 -11.053 23.584 6.657 1 22.01 ? CDH 7DU 401 A 1 HETATM 4 C CDI 7DU . . . B 2 -10.045 24.55 6.427 1 15.09 ? CDI 7DU 401 A 1 HETATM 5 C CDF 7DU . . . B 2 -10.979 24.059 9.034 1 25.9 ? CDF 7DU 401 A 1 HETATM 6 C CDE 7DU . . . B 2 -9.984 25.026 8.804 1 21.74 ? CDE 7DU 401 A 1 HETATM 7 C CDD 7DU . . . B 2 -9.52 25.273 7.507 1 16.9 ? CDD 7DU 401 A 1 HETATM 8 C CDC 7DU . . . B 2 -8.484 26.296 7.286 1 13.24 ? CDC 7DU 401 A 1 HETATM 9 N NDB 7DU . . . B 2 -8.398 26.629 5.863 1 10.36 ? NDB 7DU 401 A 1 HETATM 10 C CAZ 7DU . . . B 2 -7.442 25.844 5.062 1 11.86 ? CAZ 7DU 401 A 1 HETATM 11 O OBB 7DU . . . B 2 -6.782 24.97 5.573 1 11.63 ? OBB 7DU 401 A 1 HETATM 12 C CAY 7DU . . . B 2 -7.287 26.11 3.58 1 9.83 ? CAY 7DU 401 A 1 HETATM 13 C CAX 7DU . . . B 2 -6.12 27.013 3.38 1 7.52 ? CAX 7DU 401 A 1 HETATM 14 N NBA 7DU . . . B 2 -8.511 26.637 3.048 1 7.02 ? NBA 7DU 401 A 1 HETATM 15 C CAN 7DU . . . B 2 -9.684 25.81 2.894 1 9.98 ? CAN 7DU 401 A 1 HETATM 16 O OAP 7DU . . . B 2 -9.646 24.653 3.235 1 10.26 ? OAP 7DU 401 A 1 HETATM 17 C CAM 7DU . . . B 2 -10.969 26.375 2.322 1 7.44 ? CAM 7DU 401 A 1 HETATM 18 C CAW 7DU . . . B 2 -10.926 26.335 0.799 1 7.04 ? CAW 7DU 401 A 1 HETATM 19 C CAR 7DU . . . B 2 -10.463 24.947 0.277 1 6.95 ? CAR 7DU 401 A 1 HETATM 20 C CAQ 7DU . . . B 2 -10.407 24.92 -1.272 1 8.22 ? CAQ 7DU 401 A 1 HETATM 21 N NAV 7DU . . . B 2 -11.33 25.849 -1.893 1 6.21 ? NAV 7DU 401 A 1 HETATM 22 C CAU 7DU . . . B 2 -12.58 25.347 -2.449 1 9.05 ? CAU 7DU 401 A 1 HETATM 23 N NAT 7DU . . . B 2 -12.861 24.058 -2.339 1 7.2 ? NAT 7DU 401 A 1 HETATM 24 N NAS 7DU . . . B 2 -13.419 26.152 -3.034 1 8.8 ? NAS 7DU 401 A 1 HETATM 25 N NAO 7DU . . . B 2 -11.134 27.737 2.707 1 6.72 ? NAO 7DU 401 A 1 HETATM 26 C CAJ 7DU . . . B 2 -11.27 28.026 4.107 1 8.72 ? CAJ 7DU 401 A 1 HETATM 27 O OAL 7DU . . . B 2 -11.26 27.153 4.907 1 10.15 ? OAL 7DU 401 A 1 HETATM 28 C CAI 7DU . . . B 2 -11.428 29.471 4.538 1 8.76 ? CAI 7DU 401 A 1 HETATM 29 C CAH 7DU . . . B 2 -12.849 29.897 4.309 1 12.89 ? CAH 7DU 401 A 1 HETATM 30 N NAK 7DU . . . B 2 -10.589 30.274 3.711 1 11.41 ? NAK 7DU 401 A 1 HETATM 31 C C 7DU . . . B 2 -9.155 30.119 3.679 1 14.13 ? C 7DU 401 A 1 HETATM 32 O O 7DU . . . B 2 -8.627 29.272 4.381 1 7.95 ? O 7DU 401 A 1 HETATM 33 C CA 7DU . . . B 2 -8.334 31.046 2.781 1 14.95 ? CA 7DU 401 A 1 HETATM 34 N N 7DU . . . B 2 -7.416 31.781 3.581 1 7.92 ? N 7DU 401 A 1 HETATM 35 C CB 7DU . . . B 2 -7.586 30.328 1.687 1 9.3 ? CB 7DU 401 A 1 HETATM 36 O OG 7DU . . . B 2 -8.395 29.258 1.193 1 12.67 ? OG 7DU 401 A 1 HETATM 37 C CDR 7DU . . . B 2 -17.251 18.452 11.007 1 49.77 ? CDR 7DU 401 A 1 HETATM 38 O ODS 7DU . . . B 2 -18.148 18.246 9.897 1 46.73 ? ODS 7DU 401 A 1 HETATM 39 C CDO 7DU . . . B 2 -16.065 19.348 10.566 1 54.64 ? CDO 7DU 401 A 1 HETATM 40 C CDP 7DU . . . B 2 -14.948 19.443 11.391 1 49.98 ? CDP 7DU 401 A 1 HETATM 41 C CDQ 7DU . . . B 2 -13.841 20.256 11.011 1 45.36 ? CDQ 7DU 401 A 1 HETATM 42 C CDN 7DU . . . B 2 -16.09 20.081 9.337 1 45.42 ? CDN 7DU 401 A 1 HETATM 43 C CDM 7DU . . . B 2 -14.993 20.891 8.964 1 35.15 ? CDM 7DU 401 A 1 HETATM 44 C CDL 7DU . . . B 2 -13.86 20.98 9.797 1 40.44 ? CDL 7DU 401 A 1 HETATM 45 N NDK 7DU . . . B 2 -12.721 21.797 9.454 1 32.56 ? NDK 7DU 401 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 45 #