data_2BDH
#
_model_server_result.job_id            1LpMp3qeETe_FvgWPVN-Cw 
_model_server_result.datetime_utc      '2024-11-07 15:45:51' 
_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          2bdh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":303}' 
#
_entry.id    2BDH 
#
_exptl.entry_id    2BDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              136.174 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'P-AMINO BENZAMIDINE' 
_entity.pdbx_number_of_molecules    4 
_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            2BDH 
_cell.length_a            73.488 
_cell.length_b            73.488 
_cell.length_c            338.315 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2BDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
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 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
PISA dimeric 2 software_defined_assembly 5 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,J 1 1 
B,G,K 2 1 
C,H,L 3 1 
D,I,M 4 1 
A,E,F,J 5 1 
B,G,K 5 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' 5_545 -x+1/2,y-1/2,-z+1/4 -1 0 0 0 1 0 0 0 -1 36.744 -36.744 84.57875 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf2 A SG CYS 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 A SG CYS 111 A CYS 128 1_555 A SG CYS 211 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf4 A SG CYS 118 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 198 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf7 B SG CYS 7 B CYS 22 1_555 B SG CYS 137 B CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf8 B SG CYS 26 B CYS 42 1_555 B SG CYS 42 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf9 B SG CYS 111 B CYS 128 1_555 B SG CYS 211 B CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf10 B SG CYS 118 B CYS 136 1_555 B SG CYS 183 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf11 B SG CYS 148 B CYS 168 1_555 B SG CYS 162 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf12 B SG CYS 173 B CYS 191 1_555 B SG CYS 198 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf13 C SG CYS 7 C CYS 22 1_555 C SG CYS 137 C CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf14 C SG CYS 26 C CYS 42 1_555 C SG CYS 42 C CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf15 C SG CYS 111 C CYS 128 1_555 C SG CYS 211 C CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf16 C SG CYS 118 C CYS 136 1_555 C SG CYS 183 C CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf17 C SG CYS 148 C CYS 168 1_555 C SG CYS 162 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf18 C SG CYS 173 C CYS 191 1_555 C SG CYS 198 C CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf19 D SG CYS 7 D CYS 22 1_555 D SG CYS 137 D CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf20 D SG CYS 26 D CYS 42 1_555 D SG CYS 42 D CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf21 D SG CYS 111 D CYS 128 1_555 D SG CYS 211 D CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf22 D SG CYS 118 D CYS 136 1_555 D SG CYS 183 D CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf23 D SG CYS 148 D CYS 168 1_555 D SG CYS 162 D CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf24 D SG CYS 173 D CYS 191 1_555 D SG CYS 198 D CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc1 A NE2 HIS 10 A HIS 25 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc2 A OE2 GLU 61 A GLU 77 1_555 E ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc3 E ZN ZN . A ZN 401 1_555 B OE2 GLU 57 B GLU 74 5_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc4 E ZN ZN . A ZN 401 1_555 B OD2 ASP 59 B ASP 75 5_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? 
metalc ? metalc5 E ZN ZN . A ZN 401 1_555 B OD1 ASP 59 B ASP 75 5_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
#
_chem_comp.formula           'C7 H10 N3 1' 
_chem_comp.formula_weight    136.174 
_chem_comp.id                PBZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'P-AMINO BENZAMIDINE' 
_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
N2 C7 PBZ sing 237 n n 
N2 HN21 PBZ sing 238 n n 
N2 HN22 PBZ sing 239 n n 
N3 C7 PBZ doub 240 n n 
N3 HN31 PBZ sing 241 n n 
N3 HN32 PBZ sing 242 n n 
C7 C4 PBZ sing 243 n n 
C4 C3 PBZ sing 244 n y 
C4 C5 PBZ doub 245 n y 
C2 C3 PBZ doub 246 n y 
C2 C1 PBZ sing 247 n y 
C2 H2 PBZ sing 248 n n 
C3 H3 PBZ sing 249 n n 
C5 C6 PBZ sing 250 n y 
C5 H5 PBZ sing 251 n n 
C6 C1 PBZ doub 252 n y 
C6 H6 PBZ sing 253 n n 
C1 N1 PBZ sing 254 n n 
N1 HN11 PBZ sing 255 n n 
N1 HN12 PBZ sing 256 n n 
#
_atom_sites.entry_id                     2BDH 
_atom_sites.fract_transf_matrix[1][1]    0.013608 
_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]    0.013608 
_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]    0.002956 
_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 ZN A 1 401 1 ZN ZN2 . 
F 3 PBZ A 1 303 3 PBZ ABZ . 
G 3 PBZ B 1 301 1 PBZ ABZ . 
H 3 PBZ C 1 302 2 PBZ ABZ . 
I 3 PBZ D 1 304 4 PBZ ABZ . 
J 4 HOH A 1 402 7 HOH WAT . 
J 4 HOH A 2 403 8 HOH WAT . 
J 4 HOH A 3 404 17 HOH WAT . 
J 4 HOH A 4 405 18 HOH WAT . 
J 4 HOH A 5 406 24 HOH WAT . 
J 4 HOH A 6 407 25 HOH WAT . 
J 4 HOH A 7 408 29 HOH WAT . 
J 4 HOH A 8 409 31 HOH WAT . 
J 4 HOH A 9 410 37 HOH WAT . 
J 4 HOH A 10 411 39 HOH WAT . 
J 4 HOH A 11 412 46 HOH WAT . 
J 4 HOH A 12 413 47 HOH WAT . 
J 4 HOH A 13 414 50 HOH WAT . 
J 4 HOH A 14 415 52 HOH WAT . 
J 4 HOH A 15 416 56 HOH WAT . 
J 4 HOH A 16 417 57 HOH WAT . 
J 4 HOH A 17 418 60 HOH WAT . 
J 4 HOH A 18 419 66 HOH WAT . 
J 4 HOH A 19 420 68 HOH WAT . 
J 4 HOH A 20 421 70 HOH WAT . 
J 4 HOH A 21 422 72 HOH WAT . 
J 4 HOH A 22 423 73 HOH WAT . 
J 4 HOH A 23 424 74 HOH WAT . 
J 4 HOH A 24 425 78 HOH WAT . 
J 4 HOH A 25 426 84 HOH WAT . 
J 4 HOH A 26 427 87 HOH WAT . 
J 4 HOH A 27 428 89 HOH WAT . 
J 4 HOH A 28 429 90 HOH WAT . 
J 4 HOH A 29 430 92 HOH WAT . 
J 4 HOH A 30 431 93 HOH WAT . 
J 4 HOH A 31 432 95 HOH WAT . 
J 4 HOH A 32 433 98 HOH WAT . 
J 4 HOH A 33 434 102 HOH WAT . 
J 4 HOH A 34 435 107 HOH WAT . 
J 4 HOH A 35 436 111 HOH WAT . 
K 4 HOH B 1 302 3 HOH WAT . 
K 4 HOH B 2 303 4 HOH WAT . 
K 4 HOH B 3 304 5 HOH WAT . 
K 4 HOH B 4 305 9 HOH WAT . 
K 4 HOH B 5 306 10 HOH WAT . 
K 4 HOH B 6 307 11 HOH WAT . 
K 4 HOH B 7 308 19 HOH WAT . 
K 4 HOH B 8 309 21 HOH WAT . 
K 4 HOH B 9 310 22 HOH WAT . 
K 4 HOH B 10 311 33 HOH WAT . 
K 4 HOH B 11 312 38 HOH WAT . 
K 4 HOH B 12 313 45 HOH WAT . 
K 4 HOH B 13 314 48 HOH WAT . 
K 4 HOH B 14 315 51 HOH WAT . 
K 4 HOH B 15 316 58 HOH WAT . 
K 4 HOH B 16 317 59 HOH WAT . 
K 4 HOH B 17 318 67 HOH WAT . 
K 4 HOH B 18 319 77 HOH WAT . 
K 4 HOH B 19 320 79 HOH WAT . 
K 4 HOH B 20 321 81 HOH WAT . 
K 4 HOH B 21 322 94 HOH WAT . 
K 4 HOH B 22 323 99 HOH WAT . 
K 4 HOH B 23 324 101 HOH WAT . 
K 4 HOH B 24 325 103 HOH WAT . 
K 4 HOH B 25 326 106 HOH WAT . 
K 4 HOH B 26 327 108 HOH WAT . 
K 4 HOH B 27 328 109 HOH WAT . 
K 4 HOH B 28 329 110 HOH WAT . 
L 4 HOH C 1 303 13 HOH WAT . 
L 4 HOH C 2 304 28 HOH WAT . 
L 4 HOH C 3 305 30 HOH WAT . 
L 4 HOH C 4 306 32 HOH WAT . 
L 4 HOH C 5 307 36 HOH WAT . 
L 4 HOH C 6 308 40 HOH WAT . 
L 4 HOH C 7 309 41 HOH WAT . 
L 4 HOH C 8 310 42 HOH WAT . 
L 4 HOH C 9 311 49 HOH WAT . 
L 4 HOH C 10 312 53 HOH WAT . 
L 4 HOH C 11 313 54 HOH WAT . 
L 4 HOH C 12 314 62 HOH WAT . 
L 4 HOH C 13 315 63 HOH WAT . 
L 4 HOH C 14 316 69 HOH WAT . 
L 4 HOH C 15 317 75 HOH WAT . 
L 4 HOH C 16 318 83 HOH WAT . 
L 4 HOH C 17 319 85 HOH WAT . 
L 4 HOH C 18 320 104 HOH WAT . 
M 4 HOH D 1 305 1 HOH WAT . 
M 4 HOH D 2 306 2 HOH WAT . 
M 4 HOH D 3 307 6 HOH WAT . 
M 4 HOH D 4 308 12 HOH WAT . 
M 4 HOH D 5 309 14 HOH WAT . 
M 4 HOH D 6 310 15 HOH WAT . 
M 4 HOH D 7 311 16 HOH WAT . 
M 4 HOH D 8 312 20 HOH WAT . 
M 4 HOH D 9 313 23 HOH WAT . 
M 4 HOH D 10 314 26 HOH WAT . 
M 4 HOH D 11 315 27 HOH WAT . 
M 4 HOH D 12 316 34 HOH WAT . 
M 4 HOH D 13 317 35 HOH WAT . 
M 4 HOH D 14 318 43 HOH WAT . 
M 4 HOH D 15 319 44 HOH WAT . 
M 4 HOH D 16 320 55 HOH WAT . 
M 4 HOH D 17 321 61 HOH WAT . 
M 4 HOH D 18 322 64 HOH WAT . 
M 4 HOH D 19 323 65 HOH WAT . 
M 4 HOH D 20 324 71 HOH WAT . 
M 4 HOH D 21 325 76 HOH WAT . 
M 4 HOH D 22 326 80 HOH WAT . 
M 4 HOH D 23 327 82 HOH WAT . 
M 4 HOH D 24 328 86 HOH WAT . 
M 4 HOH D 25 329 88 HOH WAT . 
M 4 HOH D 26 330 91 HOH WAT . 
M 4 HOH D 27 331 96 HOH WAT . 
M 4 HOH D 28 332 97 HOH WAT . 
M 4 HOH D 29 333 100 HOH WAT . 
M 4 HOH D 30 334 105 HOH WAT . 
#
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 N2 PBZ . . . F 3 27.93 33.814 20.712 1 44.23 ? N2 PBZ 303 A 1 
HETATM 2 N N3 PBZ . . . F 3 25.656 33.514 20.427 1 39.99 ? N3 PBZ 303 A 1 
HETATM 3 C C7 PBZ . . . F 3 26.851 33.028 20.706 1 43.75 ? C7 PBZ 303 A 1 
HETATM 4 C C4 PBZ . . . F 3 26.989 31.525 20.992 1 43.83 ? C4 PBZ 303 A 1 
HETATM 5 C C2 PBZ . . . F 3 26.051 29.24 20.91 1 44.97 ? C2 PBZ 303 A 1 
HETATM 6 C C3 PBZ . . . F 3 25.926 30.628 20.664 1 43.43 ? C3 PBZ 303 A 1 
HETATM 7 C C5 PBZ . . . F 3 28.179 30.996 21.577 1 45.2 ? C5 PBZ 303 A 1 
HETATM 8 C C6 PBZ . . . F 3 28.303 29.603 21.824 1 45.89 ? C6 PBZ 303 A 1 
HETATM 9 C C1 PBZ . . . F 3 27.24 28.727 21.486 1 46.56 ? C1 PBZ 303 A 1 
HETATM 10 N N1 PBZ . . . F 3 27.366 27.349 21.721 1 49.31 ? N1 PBZ 303 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           10 
#