data_5VKC
#
_model_server_result.job_id            AAVusIarQD1Jx4e9QiqlWw 
_model_server_result.datetime_utc      '2025-04-03 06:03:18' 
_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          5vkc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":403}' 
#
_entry.id    5VKC 
#
_exptl.entry_id    5VKC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              65.409 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ZINC ION' 
_entity.pdbx_number_of_molecules    10 
_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            5VKC 
_cell.length_a            63.92 
_cell.length_b            63.92 
_cell.length_c            91.4 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VKC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
_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,P 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 L N N 
? 3 M N N 
? 3 N 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
metalc ? metalc1 A NE2 HIS 55 A HIS 224 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc2 A OD2 ASP 72 A ASP 241 1_555 I ZN ZN . A ZN 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc3 A OD1 ASP 73 A ASP 242 1_555 H ZN ZN . A ZN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc4 A NE2 HIS 83 A HIS 252 1_555 F ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc5 A ND1 HIS 83 A HIS 252 1_555 G ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? 
metalc ? metalc6 A OD2 ASP 87 A ASP 256 1_555 F ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc7 A OE1 GLU 119 A GLU 288 1_555 D ZN ZN . A ZN 402 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc8 A OE2 GLU 119 A GLU 288 1_555 D ZN ZN . A ZN 402 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc9 A OE2 GLU 123 A GLU 292 1_555 M ZN ZN . B ZN 403 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc10 A OD2 ASP 127 A ASP 296 1_555 M ZN ZN . B ZN 403 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc11 A NE2 HIS 151 A HIS 320 1_555 J ZN ZN . A ZN 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc12 C N47 9EA . A 9EA 401 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc13 D ZN ZN . A ZN 402 1_555 O O HOH . A HOH 506 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc14 D ZN ZN . A ZN 402 1_555 O O HOH . A HOH 529 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc15 E ZN ZN . A ZN 403 1_565 B NE2 HIS 151 B HIS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc16 E ZN ZN . A ZN 403 1_555 P O HOH . B HOH 537 1_545 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? 
metalc ? metalc17 E ZN ZN . A ZN 403 1_555 P O HOH . B HOH 550 1_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc18 F ZN ZN . A ZN 404 1_555 O O HOH . A HOH 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc19 G ZN ZN . A ZN 405 1_555 O O HOH . A HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc20 G ZN ZN . A ZN 405 3_455 B OE2 GLU 123 B GLU 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc21 G ZN ZN . A ZN 405 3_455 B OD2 ASP 127 B ASP 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc22 H ZN ZN . A ZN 406 3_455 B OD2 ASP 72 B ASP 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc23 I ZN ZN . A ZN 407 3_455 B OD1 ASP 73 B ASP 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc24 J ZN ZN . A ZN 408 1_555 O O HOH . A HOH 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc25 J ZN ZN . A ZN 408 1_555 K N47 9EA . B 9EA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc26 J ZN ZN . A ZN 408 1_555 P O HOH . B HOH 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? 
metalc ? metalc27 B NE2 HIS 55 B HIS 224 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc28 B ND1 HIS 83 B HIS 252 1_555 M ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? 
metalc ? metalc29 B NE2 HIS 83 B HIS 252 1_555 N ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc30 B OD2 ASP 87 B ASP 256 1_555 N ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc31 B OE1 GLU 119 B GLU 288 1_555 L ZN ZN . B ZN 402 3_355 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc32 B OE2 GLU 119 B GLU 288 1_555 L ZN ZN . B ZN 402 3_355 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc33 L ZN ZN . B ZN 402 1_555 P O HOH . B HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc34 L ZN ZN . B ZN 402 1_555 P O HOH . B HOH 543 2_574 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc35 M ZN ZN . B ZN 403 1_555 P O HOH . B HOH 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc36 N ZN ZN . B ZN 404 1_555 P O HOH . B HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? 
#
_chem_comp.formula           'Zn 2' 
_chem_comp.formula_weight    65.409 
_chem_comp.id                ZN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'ZINC ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5VKC 
_atom_sites.fract_transf_matrix[1][1]    0.015645 
_atom_sites.fract_transf_matrix[1][2]    0.009032 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018065 
_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]    0.010941 
_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
C 2 9EA A 1 401 1 9EA LIG . 
D 3 ZN A 1 402 1 ZN ZN . 
E 3 ZN A 1 403 2 ZN ZN . 
F 3 ZN A 1 404 3 ZN ZN . 
G 3 ZN A 1 405 4 ZN ZN . 
H 3 ZN A 1 406 5 ZN ZN . 
I 3 ZN A 1 407 6 ZN ZN . 
J 3 ZN A 1 408 2 ZN ZN . 
K 2 9EA B 1 401 1 9EA LIG . 
L 3 ZN B 1 402 1 ZN ZN . 
M 3 ZN B 1 403 3 ZN ZN . 
N 3 ZN B 1 404 4 ZN ZN . 
O 4 HOH A 1 501 16 HOH HOH . 
O 4 HOH A 2 502 108 HOH HOH . 
O 4 HOH A 3 503 9 HOH HOH . 
O 4 HOH A 4 504 103 HOH HOH . 
O 4 HOH A 5 505 109 HOH HOH . 
O 4 HOH A 6 506 48 HOH HOH . 
O 4 HOH A 7 507 63 HOH HOH . 
O 4 HOH A 8 508 35 HOH HOH . 
O 4 HOH A 9 509 49 HOH HOH . 
O 4 HOH A 10 510 7 HOH HOH . 
O 4 HOH A 11 511 94 HOH HOH . 
O 4 HOH A 12 512 46 HOH HOH . 
O 4 HOH A 13 513 124 HOH HOH . 
O 4 HOH A 14 514 6 HOH HOH . 
O 4 HOH A 15 515 67 HOH HOH . 
O 4 HOH A 16 516 99 HOH HOH . 
O 4 HOH A 17 517 97 HOH HOH . 
O 4 HOH A 18 518 29 HOH HOH . 
O 4 HOH A 19 519 84 HOH HOH . 
O 4 HOH A 20 520 69 HOH HOH . 
O 4 HOH A 21 521 11 HOH HOH . 
O 4 HOH A 22 522 12 HOH HOH . 
O 4 HOH A 23 523 28 HOH HOH . 
O 4 HOH A 24 524 26 HOH HOH . 
O 4 HOH A 25 525 100 HOH HOH . 
O 4 HOH A 26 526 120 HOH HOH . 
O 4 HOH A 27 527 45 HOH HOH . 
O 4 HOH A 28 528 34 HOH HOH . 
O 4 HOH A 29 529 47 HOH HOH . 
O 4 HOH A 30 530 107 HOH HOH . 
O 4 HOH A 31 531 18 HOH HOH . 
O 4 HOH A 32 532 115 HOH HOH . 
O 4 HOH A 33 533 43 HOH HOH . 
O 4 HOH A 34 534 81 HOH HOH . 
O 4 HOH A 35 535 30 HOH HOH . 
O 4 HOH A 36 536 70 HOH HOH . 
O 4 HOH A 37 537 118 HOH HOH . 
O 4 HOH A 38 538 72 HOH HOH . 
O 4 HOH A 39 539 90 HOH HOH . 
O 4 HOH A 40 540 54 HOH HOH . 
O 4 HOH A 41 541 36 HOH HOH . 
O 4 HOH A 42 542 112 HOH HOH . 
O 4 HOH A 43 543 4 HOH HOH . 
O 4 HOH A 44 544 117 HOH HOH . 
O 4 HOH A 45 545 121 HOH HOH . 
O 4 HOH A 46 546 87 HOH HOH . 
O 4 HOH A 47 547 39 HOH HOH . 
O 4 HOH A 48 548 24 HOH HOH . 
O 4 HOH A 49 549 41 HOH HOH . 
O 4 HOH A 50 550 50 HOH HOH . 
O 4 HOH A 51 551 95 HOH HOH . 
O 4 HOH A 52 552 21 HOH HOH . 
O 4 HOH A 53 553 40 HOH HOH . 
O 4 HOH A 54 554 33 HOH HOH . 
O 4 HOH A 55 555 92 HOH HOH . 
O 4 HOH A 56 556 88 HOH HOH . 
P 4 HOH B 1 501 101 HOH HOH . 
P 4 HOH B 2 502 57 HOH HOH . 
P 4 HOH B 3 503 102 HOH HOH . 
P 4 HOH B 4 504 110 HOH HOH . 
P 4 HOH B 5 505 60 HOH HOH . 
P 4 HOH B 6 506 1 HOH HOH . 
P 4 HOH B 7 507 10 HOH HOH . 
P 4 HOH B 8 508 13 HOH HOH . 
P 4 HOH B 9 509 104 HOH HOH . 
P 4 HOH B 10 510 83 HOH HOH . 
P 4 HOH B 11 511 119 HOH HOH . 
P 4 HOH B 12 512 8 HOH HOH . 
P 4 HOH B 13 513 19 HOH HOH . 
P 4 HOH B 14 514 122 HOH HOH . 
P 4 HOH B 15 515 3 HOH HOH . 
P 4 HOH B 16 516 123 HOH HOH . 
P 4 HOH B 17 517 82 HOH HOH . 
P 4 HOH B 18 518 59 HOH HOH . 
P 4 HOH B 19 519 22 HOH HOH . 
P 4 HOH B 20 520 32 HOH HOH . 
P 4 HOH B 21 521 73 HOH HOH . 
P 4 HOH B 22 522 96 HOH HOH . 
P 4 HOH B 23 523 25 HOH HOH . 
P 4 HOH B 24 524 91 HOH HOH . 
P 4 HOH B 25 525 85 HOH HOH . 
P 4 HOH B 26 526 66 HOH HOH . 
P 4 HOH B 27 527 105 HOH HOH . 
P 4 HOH B 28 528 17 HOH HOH . 
P 4 HOH B 29 529 61 HOH HOH . 
P 4 HOH B 30 530 75 HOH HOH . 
P 4 HOH B 31 531 114 HOH HOH . 
P 4 HOH B 32 532 62 HOH HOH . 
P 4 HOH B 33 533 64 HOH HOH . 
P 4 HOH B 34 534 74 HOH HOH . 
P 4 HOH B 35 535 65 HOH HOH . 
P 4 HOH B 36 536 76 HOH HOH . 
P 4 HOH B 37 537 52 HOH HOH . 
P 4 HOH B 38 538 56 HOH HOH . 
P 4 HOH B 39 539 44 HOH HOH . 
P 4 HOH B 40 540 38 HOH HOH . 
P 4 HOH B 41 541 55 HOH HOH . 
P 4 HOH B 42 542 53 HOH HOH . 
P 4 HOH B 43 543 58 HOH HOH . 
P 4 HOH B 44 544 86 HOH HOH . 
P 4 HOH B 45 545 77 HOH HOH . 
P 4 HOH B 46 546 15 HOH HOH . 
P 4 HOH B 47 547 14 HOH HOH . 
P 4 HOH B 48 548 42 HOH HOH . 
P 4 HOH B 49 549 2 HOH HOH . 
P 4 HOH B 50 550 51 HOH HOH . 
P 4 HOH B 51 551 116 HOH HOH . 
P 4 HOH B 52 552 68 HOH HOH . 
P 4 HOH B 53 553 89 HOH HOH . 
P 4 HOH B 54 554 80 HOH HOH . 
P 4 HOH B 55 555 78 HOH HOH . 
P 4 HOH B 56 556 5 HOH HOH . 
P 4 HOH B 57 557 37 HOH HOH . 
P 4 HOH B 58 558 93 HOH HOH . 
P 4 HOH B 59 559 23 HOH HOH . 
P 4 HOH B 60 560 27 HOH HOH . 
P 4 HOH B 61 561 31 HOH HOH . 
P 4 HOH B 62 562 79 HOH HOH . 
P 4 HOH B 63 563 98 HOH HOH . 
P 4 HOH B 64 564 71 HOH HOH . 
P 4 HOH B 65 565 111 HOH HOH . 
P 4 HOH B 66 566 106 HOH HOH . 
P 4 HOH B 67 567 20 HOH HOH . 
P 4 HOH B 68 568 113 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           ZN 
_atom_site.label_atom_id         ZN 
_atom_site.label_comp_id         ZN 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         E 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               -33.132 
_atom_site.Cartn_y               2.652 
_atom_site.Cartn_z               14.824 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        54.13 
_atom_site.pdbx_formal_charge    2 
_atom_site.auth_atom_id          ZN 
_atom_site.auth_comp_id          ZN 
_atom_site.auth_seq_id           403 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           1 
#