data_4NM5
#
_model_server_result.job_id            '_vHBV5Ae-BWvr70pOE94fA' 
_model_server_result.datetime_utc      '2024-10-11 00:28:26' 
_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          4nm5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":404}' 
#
_entry.id    4NM5 
#
_exptl.entry_id    4NM5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            4NM5 
_cell.length_a            81.727 
_cell.length_b            81.727 
_cell.length_c            280.937 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NM5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M 2 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' 10_664 -y+1,-x+1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 40.8635 70.777658 -46.822833 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 E N N 
? 5 F N N 
? 5 G N N 
? 5 H 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 C C PRO 5 C PRO 1571 1_555 C N TPO 6 C TPO 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 C C TPO 6 C TPO 1572 1_555 C N PRO 7 C PRO 1573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
metalc ? metalc1 A OD1 ASN 174 A ASN 186 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc2 A OD2 ASP 188 A ASP 200 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc3 A OD1 ASP 188 A ASP 200 1_555 J MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc4 D O1A ADP . A ADP 401 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc5 D O1B ADP . A ADP 401 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc6 D O2B ADP . A ADP 401 1_555 J MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc7 I MG MG . A MG 406 1_555 L O HOH . A HOH 572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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
C1 O1 GOL sing 173 n n 
C1 C2 GOL sing 174 n n 
C1 H11 GOL sing 175 n n 
C1 H12 GOL sing 176 n n 
O1 HO1 GOL sing 177 n n 
C2 O2 GOL sing 178 n n 
C2 C3 GOL sing 179 n n 
C2 H2 GOL sing 180 n n 
O2 HO2 GOL sing 181 n n 
C3 O3 GOL sing 182 n n 
C3 H31 GOL sing 183 n n 
C3 H32 GOL sing 184 n n 
O3 HO3 GOL sing 185 n n 
#
_atom_sites.entry_id                     4NM5 
_atom_sites.fract_transf_matrix[1][1]    0.012236 
_atom_sites.fract_transf_matrix[1][2]    0.007064 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014129 
_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]    0.00356 
_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
D 4 ADP A 1 401 1 ADP ADP . 
E 5 GOL A 1 402 1 GOL GOL . 
F 5 GOL A 1 403 2 GOL GOL . 
G 5 GOL A 1 404 3 GOL GOL . 
H 5 GOL A 1 405 4 GOL GOL . 
I 6 MG A 1 406 1 MG MG . 
J 6 MG A 1 407 2 MG MG . 
K 7 CL A 1 408 1 CL CL . 
L 8 HOH A 1 501 1 HOH HOH . 
L 8 HOH A 2 502 2 HOH HOH . 
L 8 HOH A 3 503 3 HOH HOH . 
L 8 HOH A 4 504 4 HOH HOH . 
L 8 HOH A 5 505 5 HOH HOH . 
L 8 HOH A 6 506 6 HOH HOH . 
L 8 HOH A 7 507 7 HOH HOH . 
L 8 HOH A 8 508 8 HOH HOH . 
L 8 HOH A 9 509 9 HOH HOH . 
L 8 HOH A 10 510 10 HOH HOH . 
L 8 HOH A 11 511 11 HOH HOH . 
L 8 HOH A 12 512 12 HOH HOH . 
L 8 HOH A 13 513 13 HOH HOH . 
L 8 HOH A 14 514 14 HOH HOH . 
L 8 HOH A 15 515 15 HOH HOH . 
L 8 HOH A 16 516 16 HOH HOH . 
L 8 HOH A 17 517 17 HOH HOH . 
L 8 HOH A 18 518 18 HOH HOH . 
L 8 HOH A 19 519 19 HOH HOH . 
L 8 HOH A 20 520 20 HOH HOH . 
L 8 HOH A 21 521 21 HOH HOH . 
L 8 HOH A 22 522 22 HOH HOH . 
L 8 HOH A 23 523 23 HOH HOH . 
L 8 HOH A 24 524 24 HOH HOH . 
L 8 HOH A 25 525 25 HOH HOH . 
L 8 HOH A 26 526 26 HOH HOH . 
L 8 HOH A 27 527 27 HOH HOH . 
L 8 HOH A 28 528 28 HOH HOH . 
L 8 HOH A 29 529 29 HOH HOH . 
L 8 HOH A 30 530 30 HOH HOH . 
L 8 HOH A 31 531 31 HOH HOH . 
L 8 HOH A 32 532 32 HOH HOH . 
L 8 HOH A 33 533 33 HOH HOH . 
L 8 HOH A 34 534 34 HOH HOH . 
L 8 HOH A 35 535 35 HOH HOH . 
L 8 HOH A 36 536 36 HOH HOH . 
L 8 HOH A 37 537 37 HOH HOH . 
L 8 HOH A 38 538 38 HOH HOH . 
L 8 HOH A 39 539 39 HOH HOH . 
L 8 HOH A 40 540 40 HOH HOH . 
L 8 HOH A 41 541 41 HOH HOH . 
L 8 HOH A 42 542 43 HOH HOH . 
L 8 HOH A 43 543 44 HOH HOH . 
L 8 HOH A 44 544 45 HOH HOH . 
L 8 HOH A 45 545 46 HOH HOH . 
L 8 HOH A 46 546 47 HOH HOH . 
L 8 HOH A 47 547 48 HOH HOH . 
L 8 HOH A 48 548 49 HOH HOH . 
L 8 HOH A 49 549 50 HOH HOH . 
L 8 HOH A 50 550 51 HOH HOH . 
L 8 HOH A 51 551 53 HOH HOH . 
L 8 HOH A 52 552 54 HOH HOH . 
L 8 HOH A 53 553 55 HOH HOH . 
L 8 HOH A 54 554 56 HOH HOH . 
L 8 HOH A 55 555 58 HOH HOH . 
L 8 HOH A 56 556 59 HOH HOH . 
L 8 HOH A 57 557 60 HOH HOH . 
L 8 HOH A 58 558 61 HOH HOH . 
L 8 HOH A 59 559 62 HOH HOH . 
L 8 HOH A 60 560 63 HOH HOH . 
L 8 HOH A 61 561 64 HOH HOH . 
L 8 HOH A 62 562 65 HOH HOH . 
L 8 HOH A 63 563 67 HOH HOH . 
L 8 HOH A 64 564 68 HOH HOH . 
L 8 HOH A 65 565 69 HOH HOH . 
L 8 HOH A 66 566 71 HOH HOH . 
L 8 HOH A 67 567 72 HOH HOH . 
L 8 HOH A 68 568 73 HOH HOH . 
L 8 HOH A 69 569 74 HOH HOH . 
L 8 HOH A 70 570 75 HOH HOH . 
L 8 HOH A 71 571 77 HOH HOH . 
L 8 HOH A 72 572 78 HOH HOH . 
L 8 HOH A 73 573 80 HOH HOH . 
L 8 HOH A 74 574 81 HOH HOH . 
L 8 HOH A 75 575 82 HOH HOH . 
L 8 HOH A 76 576 83 HOH HOH . 
L 8 HOH A 77 577 84 HOH HOH . 
L 8 HOH A 78 578 85 HOH HOH . 
L 8 HOH A 79 579 86 HOH HOH . 
L 8 HOH A 80 580 87 HOH HOH . 
L 8 HOH A 81 581 88 HOH HOH . 
L 8 HOH A 82 582 89 HOH HOH . 
L 8 HOH A 83 583 90 HOH HOH . 
L 8 HOH A 84 584 91 HOH HOH . 
L 8 HOH A 85 585 92 HOH HOH . 
L 8 HOH A 86 586 93 HOH HOH . 
L 8 HOH A 87 587 94 HOH HOH . 
L 8 HOH A 88 588 95 HOH HOH . 
L 8 HOH A 89 589 96 HOH HOH . 
L 8 HOH A 90 590 97 HOH HOH . 
L 8 HOH A 91 591 98 HOH HOH . 
L 8 HOH A 92 592 99 HOH HOH . 
L 8 HOH A 93 593 100 HOH HOH . 
L 8 HOH A 94 594 101 HOH HOH . 
L 8 HOH A 95 595 102 HOH HOH . 
L 8 HOH A 96 596 104 HOH HOH . 
L 8 HOH A 97 597 105 HOH HOH . 
L 8 HOH A 98 598 107 HOH HOH . 
L 8 HOH A 99 599 109 HOH HOH . 
L 8 HOH A 100 600 110 HOH HOH . 
L 8 HOH A 101 601 111 HOH HOH . 
L 8 HOH A 102 602 112 HOH HOH . 
L 8 HOH A 103 603 113 HOH HOH . 
L 8 HOH A 104 604 114 HOH HOH . 
L 8 HOH A 105 605 115 HOH HOH . 
L 8 HOH A 106 606 116 HOH HOH . 
L 8 HOH A 107 607 117 HOH HOH . 
L 8 HOH A 108 608 118 HOH HOH . 
L 8 HOH A 109 609 119 HOH HOH . 
L 8 HOH A 110 610 120 HOH HOH . 
L 8 HOH A 111 611 121 HOH HOH . 
M 8 HOH B 1 501 42 HOH HOH . 
M 8 HOH B 2 502 52 HOH HOH . 
M 8 HOH B 3 503 57 HOH HOH . 
M 8 HOH B 4 504 66 HOH HOH . 
M 8 HOH B 5 505 70 HOH HOH . 
M 8 HOH B 6 506 76 HOH HOH . 
M 8 HOH B 7 507 79 HOH HOH . 
M 8 HOH B 8 508 103 HOH HOH . 
M 8 HOH B 9 509 106 HOH HOH . 
M 8 HOH B 10 510 108 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 C C1 GOL . . . G 5 -10.645 18.833 -27.612 1 94.81 ? C1 GOL 404 A 1 
HETATM 2 O O1 GOL . . . G 5 -11.855 18.744 -26.893 1 90.64 ? O1 GOL 404 A 1 
HETATM 3 C C2 GOL . . . G 5 -10.258 17.452 -28.128 1 105.04 ? C2 GOL 404 A 1 
HETATM 4 O O2 GOL . . . G 5 -9.212 16.931 -27.338 1 106.3 ? O2 GOL 404 A 1 
HETATM 5 C C3 GOL . . . G 5 -9.787 17.57 -29.572 1 110.1 ? C3 GOL 404 A 1 
HETATM 6 O O3 GOL . . . G 5 -8.628 18.372 -29.621 1 111.66 ? O3 GOL 404 A 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#