data_8PVB
#
_model_server_result.job_id            y9R-Vz8cKPa4JZjNX_kAeQ 
_model_server_result.datetime_utc      '2024-10-19 12:43:39' 
_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          8pvb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":5409}' 
#
_entry.id    8PVB 
#
_exptl.entry_id    8PVB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              244.289 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            Etomidate 
_entity.pdbx_number_of_molecules    1 
_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            8PVB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PVB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5 
#
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 'point symmetry operation' ? ? 0.309017 -0.951057 0 0.951057 0.309017 0 0 0 1 214.81818 -34.02386 0 
3 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 313.55926 159.76642 0 
4 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 159.76642 313.55926 0 
5 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 -34.02386 214.81818 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      9 
_struct_asym.id                             M 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
3 oligosaccharide 
4 oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
4 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
5 ? 4 5 3 MAN BMA C1 O1 . O6 HO6 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n C NAG 1 B 1 NAG B 1 NAG 
3 n C NAG 2 B 2 NAG B 2 NAG 
4 n D NAG 1 C 1 NAG C 1 NAG 
4 n D NAG 2 C 2 NAG C 2 NAG 
4 n D BMA 3 C 3 BMA C 3 BMA 
4 n D MAN 4 C 4 MAN C 4 MAN 
4 n D MAN 5 C 5 MAN C 5 MAN 
#
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 B SG CYS 409 O CYS 409 1_555 B SG CYS 483 O CYS 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
covale ? covale1 A ND2 ASN 135 A ASN 80 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? 
covale ? covale2 A ND2 ASN 204 A ASN 149 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? 
covale ? covale3 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? 
covale ? covale4 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? 
covale ? covale5 D O4 NAG . C NAG 2 1_555 D C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? 
covale ? covale6 D O3 BMA . C BMA 3 1_555 D C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? 
covale ? covale7 D O6 BMA . C BMA 3 1_555 D C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? 
#
_chem_comp.formula           'C14 H16 N2 O2' 
_chem_comp.formula_weight    244.289 
_chem_comp.id                V8D 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              Etomidate 
_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
C14 C16 V8D doub 531 n y 
C14 C10 V8D sing 532 n y 
C16 C15 V8D sing 533 n y 
C10 C06 V8D doub 534 n y 
C15 C11 V8D doub 535 n y 
O02 C13 V8D doub 536 n n 
C17 C18 V8D sing 537 n n 
C17 O01 V8D sing 538 n n 
C06 C11 V8D sing 539 n y 
C06 C05 V8D sing 540 n n 
C13 O01 V8D sing 541 n n 
C13 C08 V8D sing 542 n n 
C05 C07 V8D sing 543 n n 
C05 N03 V8D sing 544 n n 
C08 N03 V8D sing 545 n y 
C08 C12 V8D doub 546 n y 
N03 C09 V8D sing 547 n y 
C12 N04 V8D sing 548 n y 
C09 N04 V8D doub 549 n y 
C05 H1 V8D sing 550 n n 
C07 H2 V8D sing 551 n n 
C07 H3 V8D sing 552 n n 
C07 H4 V8D sing 553 n n 
C09 H5 V8D sing 554 n n 
C10 H6 V8D sing 555 n n 
C11 H7 V8D sing 556 n n 
C12 H8 V8D sing 557 n n 
C14 H9 V8D sing 558 n n 
C15 H10 V8D sing 559 n n 
C16 H11 V8D sing 560 n n 
C17 H12 V8D sing 561 n n 
C17 H13 V8D sing 562 n n 
C18 H14 V8D sing 563 n n 
C18 H15 V8D sing 564 n n 
C18 H16 V8D sing 565 n n 
#
_atom_sites.entry_id                     8PVB 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 5 R16 A 1 5401 5401 R16 R16 . 
F 6 D10 A 1 5402 5402 D10 D10 . 
G 6 D10 A 1 5403 5403 D10 D10 . 
H 6 D10 A 1 5404 5404 D10 D10 . 
I 6 D10 A 1 5405 5406 D10 D10 . 
J 7 HSM A 1 5406 5408 HSM HSM . 
K 8 CL A 1 5407 5409 CL CL . 
L 8 CL A 1 5408 5410 CL CL . 
M 9 V8D A 1 5409 5501 V8D V8D . 
#
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 C05 V8D . . . M 9 118.613 141.862 111.435 1 76.62 ? C05 V8D 5409 A 1 
HETATM 2 C C06 V8D . . . M 9 118.1 142.107 112.839 1 77.34 ? C06 V8D 5409 A 1 
HETATM 3 C C07 V8D . . . M 9 120.082 141.491 111.402 1 76.62 ? C07 V8D 5409 A 1 
HETATM 4 C C08 V8D . . . M 9 116.567 141.052 110.124 1 77.33 ? C08 V8D 5409 A 1 
HETATM 5 C C09 V8D . . . M 9 118.073 139.517 110.618 1 76.74 ? C09 V8D 5409 A 1 
HETATM 6 C C10 V8D . . . M 9 118.345 143.324 113.466 1 77.82 ? C10 V8D 5409 A 1 
HETATM 7 C C11 V8D . . . M 9 117.394 141.128 113.527 1 77.13 ? C11 V8D 5409 A 1 
HETATM 8 C C12 V8D . . . M 9 116.209 139.826 109.631 1 76.17 ? C12 V8D 5409 A 1 
HETATM 9 C C13 V8D . . . M 9 115.892 142.34 110.002 1 76.61 ? C13 V8D 5409 A 1 
HETATM 10 C C14 V8D . . . M 9 117.899 143.557 114.758 1 77.84 ? C14 V8D 5409 A 1 
HETATM 11 C C15 V8D . . . M 9 116.94 141.378 114.809 1 78.39 ? C15 V8D 5409 A 1 
HETATM 12 C C16 V8D . . . M 9 117.189 142.586 115.423 1 78.43 ? C16 V8D 5409 A 1 
HETATM 13 C C17 V8D . . . M 9 113.874 143.392 109.201 1 76.29 ? C17 V8D 5409 A 1 
HETATM 14 C C18 V8D . . . M 9 113.762 143.692 107.769 1 76.63 ? C18 V8D 5409 A 1 
HETATM 15 N N03 V8D . . . M 9 117.786 140.844 110.752 1 77.05 ? N03 V8D 5409 A 1 
HETATM 16 N N04 V8D . . . M 9 117.15 138.89 109.944 1 75.17 ? N04 V8D 5409 A 1 
HETATM 17 O O01 V8D . . . M 9 114.758 142.233 109.315 1 76.07 ? O01 V8D 5409 A 1 
HETATM 18 O O02 V8D . . . M 9 116.312 143.375 110.454 1 76.23 ? O02 V8D 5409 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           347 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#