data_5VCL
#
_model_server_result.job_id            zgz1AEdf1IwZI14DkOPxPQ 
_model_server_result.datetime_utc      '2024-11-25 13:57:02' 
_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          5vcl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":309}' 
#
_entry.id    5VCL 
#
_exptl.entry_id    5VCL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    6 
_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            5VCL 
_cell.length_a            67.207 
_cell.length_b            75.876 
_cell.length_c            105.211 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VCL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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
? 5 G N N 
? 5 H N N 
? 5 I N N 
? 5 J N N 
? 5 K N N 
? 5 L 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
disulf ? disulf1 A SG CYS 102 A CYS 101 1_555 A SG CYS 165 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
disulf ? disulf2 A SG CYS 204 A CYS 203 1_555 A SG CYS 260 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc1 A OG1 THR 11 A THR 10 1_555 H NA NA . A NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.007 ? 
metalc ? metalc2 A OD2 ASP 30 A ASP 29 1_555 G NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc3 A OG SER 39 A SER 38 1_555 L NA NA . A NA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.061 ? 
metalc ? metalc4 A OD1 ASP 40 A ASP 39 1_555 L NA NA . A NA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? 
metalc ? metalc5 A OD1 ASN 78 A ASN 77 1_555 I NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc6 A OE2 GLU 117 A GLU 116 1_555 I NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? 
metalc ? metalc7 A OE1 GLN 157 A GLN 156 1_555 J NA NA . A NA 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc8 A O LEU 180 A LEU 179 1_555 G NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? 
metalc ? metalc9 A OH TYR 210 A TYR 209 1_555 G NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? 
metalc ? metalc10 H NA NA . A NA 305 1_555 B O MET 54 B MET 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? 
metalc ? metalc11 I NA NA . A NA 306 1_555 C OG1 THR 6 P THR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? 
metalc ? metalc12 I NA NA . A NA 306 1_555 C O LEU 7 P LEU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? 
#
_chem_comp.formula           'Na 1' 
_chem_comp.formula_weight    22.99 
_chem_comp.id                NA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SODIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5VCL 
_atom_sites.fract_transf_matrix[1][1]    0.014879 
_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]    0.013179 
_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]    0.009505 
_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 GOL A 1 301 1 GOL GOL . 
E 4 GOL A 1 302 2 GOL GOL . 
F 4 GOL A 1 303 4 GOL GOL . 
G 5 NA A 1 304 1 NA NA . 
H 5 NA A 1 305 2 NA NA . 
I 5 NA A 1 306 3 NA NA . 
J 5 NA A 1 307 4 NA NA . 
K 5 NA A 1 308 5 NA NA . 
L 5 NA A 1 309 7 NA NA . 
M 4 GOL B 1 101 3 GOL GOL . 
N 6 HOH A 1 401 136 HOH HOH . 
N 6 HOH A 2 402 117 HOH HOH . 
N 6 HOH A 3 403 124 HOH HOH . 
N 6 HOH A 4 404 175 HOH HOH . 
N 6 HOH A 5 405 10 HOH HOH . 
N 6 HOH A 6 406 45 HOH HOH . 
N 6 HOH A 7 407 57 HOH HOH . 
N 6 HOH A 8 408 52 HOH HOH . 
N 6 HOH A 9 409 135 HOH HOH . 
N 6 HOH A 10 410 66 HOH HOH . 
N 6 HOH A 11 411 120 HOH HOH . 
N 6 HOH A 12 412 60 HOH HOH . 
N 6 HOH A 13 413 2 HOH HOH . 
N 6 HOH A 14 414 40 HOH HOH . 
N 6 HOH A 15 415 116 HOH HOH . 
N 6 HOH A 16 416 31 HOH HOH . 
N 6 HOH A 17 417 33 HOH HOH . 
N 6 HOH A 18 418 26 HOH HOH . 
N 6 HOH A 19 419 113 HOH HOH . 
N 6 HOH A 20 420 7 HOH HOH . 
N 6 HOH A 21 421 69 HOH HOH . 
N 6 HOH A 22 422 32 HOH HOH . 
N 6 HOH A 23 423 14 HOH HOH . 
N 6 HOH A 24 424 48 HOH HOH . 
N 6 HOH A 25 425 84 HOH HOH . 
N 6 HOH A 26 426 43 HOH HOH . 
N 6 HOH A 27 427 70 HOH HOH . 
N 6 HOH A 28 428 38 HOH HOH . 
N 6 HOH A 29 429 19 HOH HOH . 
N 6 HOH A 30 430 18 HOH HOH . 
N 6 HOH A 31 431 1 HOH HOH . 
N 6 HOH A 32 432 133 HOH HOH . 
N 6 HOH A 33 433 149 HOH HOH . 
N 6 HOH A 34 434 158 HOH HOH . 
N 6 HOH A 35 435 6 HOH HOH . 
N 6 HOH A 36 436 11 HOH HOH . 
N 6 HOH A 37 437 176 HOH HOH . 
N 6 HOH A 38 438 47 HOH HOH . 
N 6 HOH A 39 439 41 HOH HOH . 
N 6 HOH A 40 440 142 HOH HOH . 
N 6 HOH A 41 441 88 HOH HOH . 
N 6 HOH A 42 442 50 HOH HOH . 
N 6 HOH A 43 443 172 HOH HOH . 
N 6 HOH A 44 444 170 HOH HOH . 
N 6 HOH A 45 445 107 HOH HOH . 
N 6 HOH A 46 446 118 HOH HOH . 
N 6 HOH A 47 447 39 HOH HOH . 
N 6 HOH A 48 448 13 HOH HOH . 
N 6 HOH A 49 449 34 HOH HOH . 
N 6 HOH A 50 450 147 HOH HOH . 
N 6 HOH A 51 451 75 HOH HOH . 
N 6 HOH A 52 452 121 HOH HOH . 
N 6 HOH A 53 453 3 HOH HOH . 
N 6 HOH A 54 454 25 HOH HOH . 
N 6 HOH A 55 455 134 HOH HOH . 
N 6 HOH A 56 456 37 HOH HOH . 
N 6 HOH A 57 457 64 HOH HOH . 
N 6 HOH A 58 458 29 HOH HOH . 
N 6 HOH A 59 459 86 HOH HOH . 
N 6 HOH A 60 460 21 HOH HOH . 
N 6 HOH A 61 461 35 HOH HOH . 
N 6 HOH A 62 462 125 HOH HOH . 
N 6 HOH A 63 463 152 HOH HOH . 
N 6 HOH A 64 464 23 HOH HOH . 
N 6 HOH A 65 465 163 HOH HOH . 
N 6 HOH A 66 466 110 HOH HOH . 
N 6 HOH A 67 467 58 HOH HOH . 
N 6 HOH A 68 468 126 HOH HOH . 
N 6 HOH A 69 469 49 HOH HOH . 
N 6 HOH A 70 470 12 HOH HOH . 
N 6 HOH A 71 471 8 HOH HOH . 
N 6 HOH A 72 472 79 HOH HOH . 
N 6 HOH A 73 473 146 HOH HOH . 
N 6 HOH A 74 474 28 HOH HOH . 
N 6 HOH A 75 475 148 HOH HOH . 
N 6 HOH A 76 476 159 HOH HOH . 
N 6 HOH A 77 477 153 HOH HOH . 
N 6 HOH A 78 478 122 HOH HOH . 
N 6 HOH A 79 479 131 HOH HOH . 
N 6 HOH A 80 480 171 HOH HOH . 
N 6 HOH A 81 481 160 HOH HOH . 
N 6 HOH A 82 482 91 HOH HOH . 
N 6 HOH A 83 483 97 HOH HOH . 
N 6 HOH A 84 484 141 HOH HOH . 
N 6 HOH A 85 485 102 HOH HOH . 
N 6 HOH A 86 486 168 HOH HOH . 
N 6 HOH A 87 487 137 HOH HOH . 
N 6 HOH A 88 488 143 HOH HOH . 
N 6 HOH A 89 489 145 HOH HOH . 
N 6 HOH A 90 490 164 HOH HOH . 
N 6 HOH A 91 491 95 HOH HOH . 
N 6 HOH A 92 492 100 HOH HOH . 
N 6 HOH A 93 493 61 HOH HOH . 
N 6 HOH A 94 494 90 HOH HOH . 
N 6 HOH A 95 495 106 HOH HOH . 
O 6 HOH B 1 201 119 HOH HOH . 
O 6 HOH B 2 202 30 HOH HOH . 
O 6 HOH B 3 203 130 HOH HOH . 
O 6 HOH B 4 204 81 HOH HOH . 
O 6 HOH B 5 205 114 HOH HOH . 
O 6 HOH B 6 206 15 HOH HOH . 
O 6 HOH B 7 207 24 HOH HOH . 
O 6 HOH B 8 208 72 HOH HOH . 
O 6 HOH B 9 209 36 HOH HOH . 
O 6 HOH B 10 210 129 HOH HOH . 
O 6 HOH B 11 211 92 HOH HOH . 
O 6 HOH B 12 212 166 HOH HOH . 
O 6 HOH B 13 213 59 HOH HOH . 
O 6 HOH B 14 214 17 HOH HOH . 
O 6 HOH B 15 215 140 HOH HOH . 
O 6 HOH B 16 216 101 HOH HOH . 
O 6 HOH B 17 217 132 HOH HOH . 
O 6 HOH B 18 218 127 HOH HOH . 
O 6 HOH B 19 219 115 HOH HOH . 
O 6 HOH B 20 220 165 HOH HOH . 
O 6 HOH B 21 221 169 HOH HOH . 
O 6 HOH B 22 222 157 HOH HOH . 
P 6 HOH P 1 101 55 HOH HOH . 
P 6 HOH P 2 102 111 HOH HOH . 
P 6 HOH P 3 103 109 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NA 
_atom_site.label_atom_id         NA 
_atom_site.label_comp_id         NA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         L 
_atom_site.label_entity_id       5 
_atom_site.Cartn_x               24.931 
_atom_site.Cartn_y               1.146 
_atom_site.Cartn_z               7.465 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        43.24 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           309 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           1 
#