data_5BV5
#
_model_server_result.job_id            Z559k7eoe8wzYPh8q7it0A 
_model_server_result.datetime_utc      '2024-11-01 13:31:13' 
_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          5bv5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":501}' 
#
_entry.id    5BV5 
#
_exptl.entry_id    5BV5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              144.173 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            4-PHENYL-1H-IMIDAZOLE 
_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          101.18 
_cell.angle_gamma         90 
_cell.entry_id            5BV5 
_cell.length_a            64.486 
_cell.length_b            137.871 
_cell.length_c            91.779 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5BV5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
PISA tetrameric 4 software_defined_assembly 5 
PISA tetrameric 4 software_defined_assembly 6 
PISA dimeric 2 software_defined_assembly 7 
PISA dimeric 2 software_defined_assembly 8 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,N 1 1 
B,G,H,I,O 2 1 
C,J,K,P 3 1 
D,L,M,Q 4 1 
B,C,G,H,I,J,K,O,P 5 1 
A,D,E,F,L,M,N,Q 5 2 
B,G,H,I,O 6 1 
D,L,M,Q 6 2 
A,E,F,N 6 4 
C,J,K,P 6 5 
A,E,F,N 7 1 
C,J,K,P 7 3 
B,G,H,I,O 8 1 
D,L,M,Q 8 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' 1_454 x-1,y,z-1 1 0 0 0 1 0 0 0 1 -46.690793 0 -90.0373 
3 'crystal symmetry operation' 1_656 x+1,y,z+1 1 0 0 0 1 0 0 0 1 46.690793 0 90.0373 
4 'crystal symmetry operation' 2_444 -x-1,y-1/2,-z-1 -1 0 0 0 1 0 0 0 -1 -46.690793 -68.9355 -90.0373 
5 'crystal symmetry operation' 2_343 -x-2,y-1/2,-z-2 -1 0 0 0 1 0 0 0 -1 -93.381587 -68.9355 -180.074601 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 I N N 
? 4 K N N 
? 4 M 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 NE2 HIS 317 A HIS 317 1_555 F FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? 
metalc ? metalc2 F FE HEM . A HEM 602 1_555 N O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc3 B NE2 HIS 317 B HIS 317 1_555 H FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? 
metalc ? metalc4 H FE HEM . B HEM 602 1_555 I N3 PIM . B PIM 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? 
metalc ? metalc5 C NE2 HIS 317 D HIS 317 1_555 J FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? 
metalc ? metalc6 J FE HEM . D HEM 500 1_555 K N3 PIM . D PIM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
metalc ? metalc7 D NE2 HIS 317 C HIS 317 1_555 L FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
metalc ? metalc8 L FE HEM . C HEM 500 1_555 M N3 PIM . C PIM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? 
#
_chem_comp.formula           'C9 H8 N2' 
_chem_comp.formula_weight    144.173 
_chem_comp.id                PIM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-PHENYL-1H-IMIDAZOLE 
_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
N1 C2 PIM sing 329 n y 
N1 C5 PIM sing 330 n y 
N1 HN1 PIM sing 331 n n 
C2 N3 PIM doub 332 n y 
C2 H2 PIM sing 333 n n 
N3 C4 PIM sing 334 n y 
C4 C5 PIM doub 335 n y 
C4 H4 PIM sing 336 n n 
C5 C6 PIM sing 337 n y 
C6 C7 PIM doub 338 n y 
C6 C11 PIM sing 339 n y 
C7 C8 PIM sing 340 n y 
C7 H7 PIM sing 341 n n 
C8 C9 PIM doub 342 n y 
C8 H8 PIM sing 343 n n 
C9 C10 PIM sing 344 n y 
C9 H9 PIM sing 345 n n 
C10 C11 PIM doub 346 n y 
C10 H10 PIM sing 347 n n 
C11 H11 PIM sing 348 n n 
#
_atom_sites.entry_id                     5BV5 
_atom_sites.fract_transf_matrix[1][1]    0.015507 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003064 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007253 
_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]    0.011106 
_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 2 PO4 A 1 601 2 PO4 PO4 . 
F 3 HEM A 1 602 500 HEM HEM . 
G 2 PO4 B 1 601 1 PO4 PO4 . 
H 3 HEM B 1 602 500 HEM HEM . 
I 4 PIM B 1 603 501 PIM PIM . 
J 3 HEM D 1 500 500 HEM HEM . 
K 4 PIM D 1 501 501 PIM PIM . 
L 3 HEM C 1 500 500 HEM HEM . 
M 4 PIM C 1 501 501 PIM PIM . 
N 5 HOH A 1 701 9 HOH HOH . 
N 5 HOH A 2 702 1 HOH HOH . 
O 5 HOH B 1 701 4 HOH HOH . 
O 5 HOH B 2 702 11 HOH HOH . 
O 5 HOH B 3 703 5 HOH HOH . 
P 5 HOH D 1 601 10 HOH HOH . 
P 5 HOH D 2 602 7 HOH HOH . 
P 5 HOH D 3 603 2 HOH HOH . 
Q 5 HOH C 1 601 3 HOH HOH . 
Q 5 HOH C 2 602 8 HOH HOH . 
Q 5 HOH C 3 603 6 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 N N1 PIM . . . K 4 -53.493 -7.089 -52.12 1 49.25 ? N1 PIM 501 D 1 
HETATM 2 C C2 PIM . . . K 4 -54.313 -6.212 -51.493 1 48.71 ? C2 PIM 501 D 1 
HETATM 3 N N3 PIM . . . K 4 -53.614 -5.113 -51.101 1 49.7 ? N3 PIM 501 D 1 
HETATM 4 C C4 PIM . . . K 4 -52.332 -5.307 -51.495 1 49.63 ? C4 PIM 501 D 1 
HETATM 5 C C5 PIM . . . K 4 -52.28 -6.535 -52.122 1 49.14 ? C5 PIM 501 D 1 
HETATM 6 C C6 PIM . . . K 4 -51.15 -7.281 -52.749 1 48.96 ? C6 PIM 501 D 1 
HETATM 7 C C7 PIM . . . K 4 -51.351 -8.188 -53.786 1 49.33 ? C7 PIM 501 D 1 
HETATM 8 C C8 PIM . . . K 4 -50.264 -8.859 -54.344 1 49.95 ? C8 PIM 501 D 1 
HETATM 9 C C9 PIM . . . K 4 -48.974 -8.624 -53.871 1 49.38 ? C9 PIM 501 D 1 
HETATM 10 C C10 PIM . . . K 4 -48.771 -7.713 -52.839 1 49.09 ? C10 PIM 501 D 1 
HETATM 11 C C11 PIM . . . K 4 -49.858 -7.044 -52.281 1 49.22 ? C11 PIM 501 D 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           11 
#