data_7VGV
#
_model_server_result.job_id            oC_dzNdaozk7ml8l4Wrgtg 
_model_server_result.datetime_utc      '2024-11-17 19:30:56' 
_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          7vgv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":301}' 
#
_entry.id    7VGV 
#
_exptl.entry_id    7VGV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_entity.pdbx_number_of_molecules    3 
_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            7VGV 
_cell.length_a            68.4 
_cell.length_b            69.5 
_cell.length_c            231.4 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7VGV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I,J,V 1 1 
B,K,L,M,N,O,P,Q,W 2 1 
C,R,S,T,U,X 3 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
? 2 D N N 
? 2 K N N 
? 2 R 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 A NZ LYS 242 A LYS 235 1_555 D C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale2 B NZ LYS 242 B LYS 235 1_555 K C15 RET . B RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale3 C NZ LYS 242 C LYS 235 1_555 R C15 RET . C RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
#
_chem_comp.formula           'C20 H28 O' 
_chem_comp.formula_weight    284.436 
_chem_comp.id                RET 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RETINAL 
_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
C1 C2 RET sing 441 n n 
C1 C6 RET sing 442 n n 
C1 C16 RET sing 443 n n 
C1 C17 RET sing 444 n n 
C2 C3 RET sing 445 n n 
C2 H21 RET sing 446 n n 
C2 H22 RET sing 447 n n 
C3 C4 RET sing 448 n n 
C3 H31 RET sing 449 n n 
C3 H32 RET sing 450 n n 
C4 C5 RET sing 451 n n 
C4 H41 RET sing 452 n n 
C4 H42 RET sing 453 n n 
C5 C6 RET doub 454 n n 
C5 C18 RET sing 455 n n 
C6 C7 RET sing 456 n n 
C7 C8 RET doub 457 e n 
C7 H7 RET sing 458 n n 
C8 C9 RET sing 459 n n 
C8 H8 RET sing 460 n n 
C9 C10 RET doub 461 e n 
C9 C19 RET sing 462 n n 
C10 C11 RET sing 463 n n 
C10 H10 RET sing 464 n n 
C11 C12 RET doub 465 e n 
C11 H11 RET sing 466 n n 
C12 C13 RET sing 467 n n 
C12 H12 RET sing 468 n n 
C13 C14 RET doub 469 e n 
C13 C20 RET sing 470 n n 
C14 C15 RET sing 471 n n 
C14 H14 RET sing 472 n n 
C15 O1 RET doub 473 n n 
C15 H15 RET sing 474 n n 
C16 H161 RET sing 475 n n 
C16 H162 RET sing 476 n n 
C16 H163 RET sing 477 n n 
C17 H171 RET sing 478 n n 
C17 H172 RET sing 479 n n 
C17 H173 RET sing 480 n n 
C18 H181 RET sing 481 n n 
C18 H182 RET sing 482 n n 
C18 H183 RET sing 483 n n 
C19 H191 RET sing 484 n n 
C19 H192 RET sing 485 n n 
C19 H193 RET sing 486 n n 
C20 H201 RET sing 487 n n 
C20 H202 RET sing 488 n n 
C20 H203 RET sing 489 n n 
#
_atom_sites.entry_id                     7VGV 
_atom_sites.fract_transf_matrix[1][1]    0.01462 
_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]    0.014388 
_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]    0.004322 
_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 2 RET A 1 301 1 RET RET . 
E 3 HEX A 1 302 5 HEX HEX . 
F 3 HEX A 1 303 6 HEX HEX . 
G 4 DD9 A 1 304 1 DD9 DD9 . 
H 4 DD9 A 1 305 3 DD9 DD9 . 
I 5 C14 A 1 306 1 C14 C14 . 
J 6 R16 A 1 307 1 R16 R16 . 
K 2 RET B 1 301 2 RET RET . 
L 3 HEX B 1 302 2 HEX HEX . 
M 3 HEX B 1 303 3 HEX HEX . 
N 3 HEX B 1 304 4 HEX HEX . 
O 4 DD9 B 1 305 2 DD9 DD9 . 
P 5 C14 B 1 306 2 C14 C14 . 
Q 7 OCT B 1 307 1 OCT OCT . 
R 2 RET C 1 301 3 RET RET . 
S 8 CL C 1 302 1 CL CL . 
T 8 CL C 1 303 2 CL CL . 
U 3 HEX C 1 304 1 HEX HEX . 
V 9 HOH A 1 401 411 HOH HOH . 
V 9 HOH A 2 402 420 HOH HOH . 
V 9 HOH A 3 403 429 HOH HOH . 
V 9 HOH A 4 404 503 HOH HOH . 
V 9 HOH A 5 405 404 HOH HOH . 
V 9 HOH A 6 406 405 HOH HOH . 
V 9 HOH A 7 407 527 HOH HOH . 
V 9 HOH A 8 408 501 HOH HOH . 
V 9 HOH A 9 409 502 HOH HOH . 
V 9 HOH A 10 410 402 HOH HOH . 
V 9 HOH A 11 411 511 HOH HOH . 
V 9 HOH A 12 412 507 HOH HOH . 
V 9 HOH A 13 413 407 HOH HOH . 
V 9 HOH A 14 414 457 HOH HOH . 
V 9 HOH A 15 415 463 HOH HOH . 
V 9 HOH A 16 416 514 HOH HOH . 
V 9 HOH A 17 417 403 HOH HOH . 
V 9 HOH A 18 418 510 HOH HOH . 
V 9 HOH A 19 419 412 HOH HOH . 
V 9 HOH A 20 420 461 HOH HOH . 
V 9 HOH A 21 421 509 HOH HOH . 
V 9 HOH A 22 422 458 HOH HOH . 
V 9 HOH A 23 423 526 HOH HOH . 
V 9 HOH A 24 424 462 HOH HOH . 
V 9 HOH A 25 425 528 HOH HOH . 
W 9 HOH B 1 401 411 HOH HOH . 
W 9 HOH B 2 402 404 HOH HOH . 
W 9 HOH B 3 403 503 HOH HOH . 
W 9 HOH B 4 404 501 HOH HOH . 
W 9 HOH B 5 405 502 HOH HOH . 
W 9 HOH B 6 406 402 HOH HOH . 
W 9 HOH B 7 407 507 HOH HOH . 
W 9 HOH B 8 408 403 HOH HOH . 
W 9 HOH B 9 409 523 HOH HOH . 
W 9 HOH B 10 410 465 HOH HOH . 
W 9 HOH B 11 411 526 HOH HOH . 
W 9 HOH B 12 412 511 HOH HOH . 
W 9 HOH B 13 413 509 HOH HOH . 
W 9 HOH B 14 414 458 HOH HOH . 
W 9 HOH B 15 415 512 HOH HOH . 
X 9 HOH C 1 401 503 HOH HOH . 
X 9 HOH C 2 402 420 HOH HOH . 
X 9 HOH C 3 403 501 HOH HOH . 
X 9 HOH C 4 404 471 HOH HOH . 
X 9 HOH C 5 405 406 HOH HOH . 
X 9 HOH C 6 406 467 HOH HOH . 
X 9 HOH C 7 407 461 HOH HOH . 
X 9 HOH C 8 408 411 HOH HOH . 
X 9 HOH C 9 409 410 HOH HOH . 
X 9 HOH C 10 410 458 HOH HOH . 
X 9 HOH C 11 411 417 HOH HOH . 
X 9 HOH C 12 412 439 HOH HOH . 
X 9 HOH C 13 413 514 HOH HOH . 
X 9 HOH C 14 414 434 HOH HOH . 
X 9 HOH C 15 415 469 HOH HOH . 
X 9 HOH C 16 416 403 HOH HOH . 
X 9 HOH C 17 417 407 HOH HOH . 
X 9 HOH C 18 418 404 HOH HOH . 
X 9 HOH C 19 419 502 HOH HOH . 
X 9 HOH C 20 420 402 HOH HOH . 
X 9 HOH C 21 421 429 HOH HOH . 
X 9 HOH C 22 422 412 HOH HOH . 
X 9 HOH C 23 423 465 HOH HOH . 
X 9 HOH C 24 424 470 HOH HOH . 
X 9 HOH C 25 425 421 HOH HOH . 
X 9 HOH C 26 426 464 HOH HOH . 
X 9 HOH C 27 427 529 HOH HOH . 
X 9 HOH C 28 428 468 HOH HOH . 
X 9 HOH C 29 429 472 HOH HOH . 
X 9 HOH C 30 430 466 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 RET . . . K 2 -25.284 4.743 -5.324 1 43.28 ? C1 RET 301 B 1 
HETATM 2 C C2 RET . . . K 2 -24.383 3.845 -6.207 1 34.74 ? C2 RET 301 B 1 
HETATM 3 C C3 RET . . . K 2 -24.44 2.367 -5.955 1 39.54 ? C3 RET 301 B 1 
HETATM 4 C C4 RET . . . K 2 -24.087 2.091 -4.529 1 40.59 ? C4 RET 301 B 1 
HETATM 5 C C5 RET . . . K 2 -24.654 3.061 -3.54 1 43.17 ? C5 RET 301 B 1 
HETATM 6 C C6 RET . . . K 2 -25.377 4.168 -3.906 1 36.9 ? C6 RET 301 B 1 
HETATM 7 C C7 RET . . . K 2 -26.27 4.784 -2.908 1 38.58 ? C7 RET 301 B 1 
HETATM 8 C C8 RET . . . K 2 -26.934 5.942 -2.906 1 37.12 ? C8 RET 301 B 1 
HETATM 9 C C9 RET . . . K 2 -27.784 6.471 -1.874 1 37.47 ? C9 RET 301 B 1 
HETATM 10 C C10 RET . . . K 2 -28.524 7.561 -2.165 1 40.55 ? C10 RET 301 B 1 
HETATM 11 C C11 RET . . . K 2 -29.434 8.278 -1.327 1 46.69 ? C11 RET 301 B 1 
HETATM 12 C C12 RET . . . K 2 -30.206 9.312 -1.813 1 38.62 ? C12 RET 301 B 1 
HETATM 13 C C13 RET . . . K 2 -31.158 10.113 -1.071 1 45.24 ? C13 RET 301 B 1 
HETATM 14 C C14 RET . . . K 2 -31.881 11.006 -1.741 1 46.53 ? C14 RET 301 B 1 
HETATM 15 C C15 RET . . . K 2 -32.88 11.907 -1.229 1 40.44 ? C15 RET 301 B 1 
HETATM 16 C C16 RET . . . K 2 -24.681 6.156 -5.311 1 36.76 ? C16 RET 301 B 1 
HETATM 17 C C17 RET . . . K 2 -26.677 4.738 -6.004 1 33.48 ? C17 RET 301 B 1 
HETATM 18 C C18 RET . . . K 2 -24.608 2.518 -2.109 1 38.8 ? C18 RET 301 B 1 
HETATM 19 C C19 RET . . . K 2 -27.797 5.8 -0.533 1 31.49 ? C19 RET 301 B 1 
HETATM 20 C C20 RET . . . K 2 -31.272 9.893 0.408 1 36.08 ? C20 RET 301 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           226 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#