data_4NAK
#
_model_server_result.job_id            Wn4E7UtRabOOE6_SAkSQ6Q 
_model_server_result.datetime_utc      '2024-12-29 09:14:11' 
_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":"E","auth_seq_id":404}' 
#
_entry.id    4NAK 
#
_exptl.entry_id    4NAK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              112.411 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CADMIUM ION' 
_entity.pdbx_number_of_molecules    5 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 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
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           'Cd 2' 
_chem_comp.formula_weight    112.411 
_chem_comp.id                CD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CADMIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_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 . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CD 
_atom_site.label_atom_id         CD 
_atom_site.label_comp_id         CD 
_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       4 
_atom_site.Cartn_x               11.745 
_atom_site.Cartn_y               20.342 
_atom_site.Cartn_z               0 
_atom_site.occupancy             0.5 
_atom_site.B_iso_or_equiv        40.48 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CD 
_atom_site.auth_comp_id          CD 
_atom_site.auth_seq_id           404 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#