data_3AYM
#
_model_server_result.job_id            4TbQGKYNUXrUP8A9FQAhPg 
_model_server_result.datetime_utc      '2024-11-27 02:59:39' 
_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          3aym 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1000}' 
#
_entry.id    3AYM 
#
_exptl.entry_id    3AYM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_entity.pdbx_number_of_molecules    2 
_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            3AYM 
_cell.length_a            122.36 
_cell.length_b            122.36 
_cell.length_c            158.22 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3AYM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        171 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 62' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,J 1 1 
B,F,G,H,I,K 2 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
? 4 E N N 
? 4 I 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 108 A CYS 108 1_555 A SG CYS 186 A CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf2 B SG CYS 108 B CYS 108 1_555 B SG CYS 186 B CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
covale ? covale1 A NZ LYS 305 A LYS 305 1_555 E C15 RET . A RET 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? 
covale ? covale2 B NZ LYS 305 B LYS 305 1_555 I C15 RET . B RET 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.285 ? 
#
_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 515 n n 
C1 C6 RET sing 516 n n 
C1 C16 RET sing 517 n n 
C1 C17 RET sing 518 n n 
C2 C3 RET sing 519 n n 
C2 H21 RET sing 520 n n 
C2 H22 RET sing 521 n n 
C3 C4 RET sing 522 n n 
C3 H31 RET sing 523 n n 
C3 H32 RET sing 524 n n 
C4 C5 RET sing 525 n n 
C4 H41 RET sing 526 n n 
C4 H42 RET sing 527 n n 
C5 C6 RET doub 528 n n 
C5 C18 RET sing 529 n n 
C6 C7 RET sing 530 n n 
C7 C8 RET doub 531 e n 
C7 H7 RET sing 532 n n 
C8 C9 RET sing 533 n n 
C8 H8 RET sing 534 n n 
C9 C10 RET doub 535 e n 
C9 C19 RET sing 536 n n 
C10 C11 RET sing 537 n n 
C10 H10 RET sing 538 n n 
C11 C12 RET doub 539 e n 
C11 H11 RET sing 540 n n 
C12 C13 RET sing 541 n n 
C12 H12 RET sing 542 n n 
C13 C14 RET doub 543 e n 
C13 C20 RET sing 544 n n 
C14 C15 RET sing 545 n n 
C14 H14 RET sing 546 n n 
C15 O1 RET doub 547 n n 
C15 H15 RET sing 548 n n 
C16 H161 RET sing 549 n n 
C16 H162 RET sing 550 n n 
C16 H163 RET sing 551 n n 
C17 H171 RET sing 552 n n 
C17 H172 RET sing 553 n n 
C17 H173 RET sing 554 n n 
C18 H181 RET sing 555 n n 
C18 H182 RET sing 556 n n 
C18 H183 RET sing 557 n n 
C19 H191 RET sing 558 n n 
C19 H192 RET sing 559 n n 
C19 H193 RET sing 560 n n 
C20 H201 RET sing 561 n n 
C20 H202 RET sing 562 n n 
C20 H203 RET sing 563 n n 
#
_atom_sites.entry_id                     3AYM 
_atom_sites.fract_transf_matrix[1][1]    0.008173 
_atom_sites.fract_transf_matrix[1][2]    0.004718 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009437 
_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]    0.00632 
_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 PLM A 1 1001 1001 PLM PLM . 
D 3 BOG A 1 1005 1005 BOG BOG . 
E 4 RET A 1 1000 1000 RET RET . 
F 5 SO4 B 1 449 449 SO4 SO4 . 
G 6 PC1 B 1 1004 1004 PC1 PC1 . 
H 3 BOG B 1 1005 1005 BOG BOG . 
I 4 RET B 1 1000 1000 RET RET . 
J 7 HOH A 1 500 500 HOH HOH . 
J 7 HOH A 2 501 501 HOH HOH . 
J 7 HOH A 3 502 502 HOH HOH . 
J 7 HOH A 4 503 503 HOH HOH . 
J 7 HOH A 5 504 504 HOH HOH . 
J 7 HOH A 6 505 505 HOH HOH . 
J 7 HOH A 7 506 506 HOH HOH . 
J 7 HOH A 8 507 507 HOH HOH . 
J 7 HOH A 9 508 508 HOH HOH . 
J 7 HOH A 10 509 509 HOH HOH . 
J 7 HOH A 11 510 510 HOH HOH . 
J 7 HOH A 12 511 511 HOH HOH . 
J 7 HOH A 13 512 512 HOH HOH . 
J 7 HOH A 14 513 513 HOH HOH . 
J 7 HOH A 15 514 514 HOH HOH . 
J 7 HOH A 16 515 515 HOH HOH . 
J 7 HOH A 17 516 516 HOH HOH . 
J 7 HOH A 18 517 517 HOH HOH . 
J 7 HOH A 19 518 518 HOH HOH . 
J 7 HOH A 20 519 519 HOH HOH . 
J 7 HOH A 21 520 520 HOH HOH . 
J 7 HOH A 22 521 521 HOH HOH . 
J 7 HOH A 23 522 522 HOH HOH . 
J 7 HOH A 24 523 523 HOH HOH . 
J 7 HOH A 25 524 524 HOH HOH . 
J 7 HOH A 26 525 525 HOH HOH . 
J 7 HOH A 27 526 526 HOH HOH . 
J 7 HOH A 28 527 527 HOH HOH . 
J 7 HOH A 29 529 529 HOH HOH . 
K 7 HOH B 1 500 500 HOH HOH . 
K 7 HOH B 2 501 501 HOH HOH . 
K 7 HOH B 3 502 502 HOH HOH . 
K 7 HOH B 4 503 503 HOH HOH . 
K 7 HOH B 5 504 504 HOH HOH . 
K 7 HOH B 6 505 505 HOH HOH . 
K 7 HOH B 7 506 506 HOH HOH . 
K 7 HOH B 8 507 507 HOH HOH . 
K 7 HOH B 9 508 508 HOH HOH . 
K 7 HOH B 10 509 509 HOH HOH . 
K 7 HOH B 11 510 510 HOH HOH . 
K 7 HOH B 12 511 511 HOH HOH . 
K 7 HOH B 13 512 512 HOH HOH . 
K 7 HOH B 14 513 513 HOH HOH . 
K 7 HOH B 15 514 514 HOH HOH . 
K 7 HOH B 16 515 515 HOH HOH . 
K 7 HOH B 17 516 516 HOH HOH . 
K 7 HOH B 18 517 517 HOH HOH . 
K 7 HOH B 19 518 518 HOH HOH . 
K 7 HOH B 20 519 519 HOH HOH . 
K 7 HOH B 21 520 520 HOH HOH . 
K 7 HOH B 22 521 521 HOH HOH . 
K 7 HOH B 23 522 522 HOH HOH . 
K 7 HOH B 24 523 523 HOH HOH . 
K 7 HOH B 25 524 524 HOH HOH . 
K 7 HOH B 26 525 525 HOH HOH . 
K 7 HOH B 27 526 526 HOH HOH . 
K 7 HOH B 28 527 527 HOH HOH . 
K 7 HOH B 29 528 528 HOH HOH . 
K 7 HOH B 30 529 529 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 . . . E 4 19.266 44.725 61.143 1 49.63 ? C1 RET 1000 A 1 
HETATM 2 C C2 RET . . . E 4 20.391 44.067 62.026 1 48.57 ? C2 RET 1000 A 1 
HETATM 3 C C3 RET . . . E 4 19.967 43.345 63.177 1 47.89 ? C3 RET 1000 A 1 
HETATM 4 C C4 RET . . . E 4 18.982 44.109 64.032 1 51.88 ? C4 RET 1000 A 1 
HETATM 5 C C5 RET . . . E 4 17.769 44.615 63.267 1 51.69 ? C5 RET 1000 A 1 
HETATM 6 C C6 RET . . . E 4 17.866 44.88 61.941 1 50.27 ? C6 RET 1000 A 1 
HETATM 7 C C7 RET . . . E 4 16.744 45.284 61.034 1 47.65 ? C7 RET 1000 A 1 
HETATM 8 C C8 RET . . . E 4 15.681 44.538 60.907 1 45.05 ? C8 RET 1000 A 1 
HETATM 9 C C9 RET . . . E 4 14.712 44.622 59.854 1 43.16 ? C9 RET 1000 A 1 
HETATM 10 C C10 RET . . . E 4 13.919 43.526 59.835 1 41.88 ? C10 RET 1000 A 1 
HETATM 11 C C11 RET . . . E 4 13.053 42.997 58.824 1 37.05 ? C11 RET 1000 A 1 
HETATM 12 C C12 RET . . . E 4 12.628 41.746 59.06 1 35.85 ? C12 RET 1000 A 1 
HETATM 13 C C13 RET . . . E 4 12.106 40.794 58.126 1 34.8 ? C13 RET 1000 A 1 
HETATM 14 C C14 RET . . . E 4 11.504 39.691 58.578 1 33.88 ? C14 RET 1000 A 1 
HETATM 15 C C15 RET . . . E 4 11.03 38.646 57.685 1 34.28 ? C15 RET 1000 A 1 
HETATM 16 C C16 RET . . . E 4 19.814 46.135 60.806 1 49.34 ? C16 RET 1000 A 1 
HETATM 17 C C17 RET . . . E 4 19.129 43.966 59.829 1 46.89 ? C17 RET 1000 A 1 
HETATM 18 C C18 RET . . . E 4 16.542 44.764 64.129 1 53.82 ? C18 RET 1000 A 1 
HETATM 19 C C19 RET . . . E 4 14.881 45.638 58.778 1 42.57 ? C19 RET 1000 A 1 
HETATM 20 C C20 RET . . . E 4 12.404 41.012 56.67 1 30.66 ? C20 RET 1000 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          20 
_model_server_stats.element_count           20 
#