data_8JV8
#
_model_server_result.job_id            F77mk9K-m4rJM2Dkk5DrwA 
_model_server_result.datetime_utc      '2024-11-22 13:52:43' 
_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          8jv8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":403}' 
#
_entry.id    8JV8 
#
_exptl.entry_id    8JV8 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              606.434 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid' 
_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            8JV8 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8JV8 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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,N,O 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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
? 3 F N N 
? 3 I N N 
? 3 L 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 99 A CYS 119 1_555 A SG CYS 148 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 A SG CYS 109 A CYS 129 1_555 A SG CYS 132 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 A SG CYS 115 A CYS 135 1_555 A SG CYS 142 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 A SG CYS 196 A CYS 216 1_555 A SG CYS 206 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 240 A CYS 260 1_555 A SG CYS 249 A CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf6 B SG CYS 99 B CYS 119 1_555 B SG CYS 148 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf7 B SG CYS 109 B CYS 129 1_555 B SG CYS 132 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf8 B SG CYS 115 B CYS 135 1_555 B SG CYS 142 B CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf9 B SG CYS 196 B CYS 216 1_555 B SG CYS 206 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf10 B SG CYS 240 B CYS 260 1_555 B SG CYS 249 B CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf11 C SG CYS 99 C CYS 119 1_555 C SG CYS 148 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf12 C SG CYS 109 C CYS 129 1_555 C SG CYS 132 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf13 C SG CYS 115 C CYS 135 1_555 C SG CYS 142 C CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf14 C SG CYS 196 C CYS 216 1_555 C SG CYS 206 C CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf15 C SG CYS 240 C CYS 260 1_555 C SG CYS 249 C CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
covale ? covale1 A ND2 ASN 167 A ASN 187 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? 
covale ? covale2 A ND2 ASN 193 A ASN 213 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? 
covale ? covale3 B ND2 ASN 167 B ASN 187 1_555 G C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? 
covale ? covale4 B ND2 ASN 193 B ASN 213 1_555 H C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? 
covale ? covale5 C ND2 ASN 167 C ASN 187 1_555 J C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale6 C ND2 ASN 193 C ASN 213 1_555 K C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
#
_chem_comp.formula           'C18 H15 N4 O14 P S2' 
_chem_comp.formula_weight    606.434 
_chem_comp.id                20V 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "PPNDS;Pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonic acid)" 
#
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
OAF SBM 20V doub 1 n n 
OAG SBM 20V doub 2 n n 
SBM OAN 20V sing 3 n n 
SBM CBG 20V sing 4 n n 
CBG CAQ 20V doub 5 n y 
CBG CBH 20V sing 6 n y 
CAQ CBB 20V sing 7 n y 
OAJ NBJ 20V sing 8 n n 
CAR CBH 20V doub 9 n y 
CAR CAZ 20V sing 10 n y 
CBH CBI 20V sing 11 n y 
CAA CAY 20V sing 12 n n 
CBB NBJ 20V sing 13 n n 
CBB CAS 20V doub 14 n y 
NBJ OAI 20V doub 15 n n 
NAW CAY 20V doub 16 n y 
NAW CBD 20V sing 17 n y 
CAY CBA 20V sing 18 n y 
NAU CAZ 20V sing 19 n n 
NAU NAV 20V doub 20 n n 
CAZ CAP 20V doub 21 n y 
CBI CAS 20V sing 22 n y 
CBI CBF 20V doub 23 n y 
NAV CBD 20V sing 24 n n 
CBD CBE 20V doub 25 n y 
CBA OAH 20V sing 26 n n 
CBA CBC 20V doub 27 n y 
CBE CBC 20V sing 28 n y 
CBE CAT 20V sing 29 n n 
CBC CAO 20V sing 30 n n 
CAP CBF 20V sing 31 n y 
OAB CAO 20V doub 32 n n 
CBF SBL 20V sing 33 n n 
CAT OAX 20V sing 34 n n 
OAM SBL 20V doub 35 n n 
SBL OAD 20V doub 36 n n 
SBL OAE 20V sing 37 n n 
OAX PBK 20V sing 38 n n 
OAL PBK 20V doub 39 n n 
PBK OAC 20V sing 40 n n 
PBK OAK 20V sing 41 n n 
OAK H1 20V sing 42 n n 
OAC H2 20V sing 43 n n 
CAT H3 20V sing 44 n n 
CAT H4 20V sing 45 n n 
CAO H5 20V sing 46 n n 
OAH H6 20V sing 47 n n 
CAA H7 20V sing 48 n n 
CAA H8 20V sing 49 n n 
CAA H9 20V sing 50 n n 
CAR H10 20V sing 51 n n 
CAQ H11 20V sing 52 n n 
CAS H12 20V sing 53 n n 
CAP H13 20V sing 54 n n 
OAN H14 20V sing 55 n n 
OAE H15 20V sing 56 n n 
#
_atom_sites.entry_id                     8JV8 
_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
D 2 NAG A 1 401 401 NAG NAG . 
E 2 NAG A 1 402 402 NAG NAG . 
F 3 20V A 1 403 405 20V PPN . 
G 2 NAG B 1 401 401 NAG NAG . 
H 2 NAG B 1 402 402 NAG NAG . 
I 3 20V B 1 403 405 20V PPN . 
J 2 NAG C 1 401 401 NAG NAG . 
K 2 NAG C 1 402 402 NAG NAG . 
L 3 20V C 1 403 405 20V PPN . 
M 4 HOH A 1 501 404 HOH HOH . 
N 4 HOH B 1 501 404 HOH HOH . 
O 4 HOH C 1 501 404 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 O OAK 20V . . . F 3 93.628 90.449 86.041 1 182.89 ? OAK 20V 403 A 1 
HETATM 2 P PBK 20V . . . F 3 94.072 89.013 85.903 1 190.16 ? PBK 20V 403 A 1 
HETATM 3 O OAL 20V . . . F 3 92.867 88.14 85.649 1 186.08 ? OAL 20V 403 A 1 
HETATM 4 O OAC 20V . . . F 3 95.029 88.9 84.74 1 186.26 ? OAC 20V 403 A 1 
HETATM 5 O OAX 20V . . . F 3 94.819 88.544 87.297 1 185.89 ? OAX 20V 403 A 1 
HETATM 6 C CAT 20V . . . F 3 95.987 87.774 87.236 1 182.12 ? CAT 20V 403 A 1 
HETATM 7 C CBE 20V . . . F 3 95.748 86.513 86.408 1 181.45 ? CBE 20V 403 A 1 
HETATM 8 C CBC 20V . . . F 3 96.625 86.149 85.449 1 181.14 ? CBC 20V 403 A 1 
HETATM 9 C CAO 20V . . . F 3 97.856 86.985 85.186 1 182.69 ? CAO 20V 403 A 1 
HETATM 10 O OAB 20V . . . F 3 98.451 86.79 84.182 1 184.57 ? OAB 20V 403 A 1 
HETATM 11 C CBA 20V . . . F 3 96.42 85.036 84.709 1 182.26 ? CBA 20V 403 A 1 
HETATM 12 O OAH 20V . . . F 3 97.343 84.675 83.718 1 183.38 ? OAH 20V 403 A 1 
HETATM 13 C CAY 20V . . . F 3 95.297 84.261 84.939 1 182.52 ? CAY 20V 403 A 1 
HETATM 14 C CAA 20V . . . F 3 95.042 82.997 84.13 1 181.47 ? CAA 20V 403 A 1 
HETATM 15 N NAW 20V . . . F 3 94.419 84.62 85.893 1 183.77 ? NAW 20V 403 A 1 
HETATM 16 C CBD 20V . . . F 3 94.633 85.73 86.625 1 184.05 ? CBD 20V 403 A 1 
HETATM 17 N NAV 20V . . . F 3 93.672 86.083 87.64 1 186.2 ? NAV 20V 403 A 1 
HETATM 18 N NAU 20V . . . F 3 92.707 85.367 87.747 1 184.8 ? NAU 20V 403 A 1 
HETATM 19 C CAZ 20V . . . F 3 91.719 85.62 88.768 1 182.49 ? CAZ 20V 403 A 1 
HETATM 20 C CAR 20V . . . F 3 90.627 84.836 88.884 1 180.59 ? CAR 20V 403 A 1 
HETATM 21 C CBH 20V . . . F 3 89.717 85.09 89.917 1 180.11 ? CBH 20V 403 A 1 
HETATM 22 C CBG 20V . . . F 3 88.651 84.32 89.998 1 182.05 ? CBG 20V 403 A 1 
HETATM 23 S SBM 20V . . . F 3 88.518 83.017 88.75 1 187.97 ? SBM 20V 403 A 1 
HETATM 24 O OAN 20V . . . F 3 89.637 82.084 88.853 1 187.05 ? OAN 20V 403 A 1 
HETATM 25 O OAG 20V . . . F 3 87.15 82.271 88.858 1 186.09 ? OAG 20V 403 A 1 
HETATM 26 O OAF 20V . . . F 3 88.405 83.62 87.367 1 182.52 ? OAF 20V 403 A 1 
HETATM 27 C CAQ 20V . . . F 3 87.615 84.419 90.976 1 184.17 ? CAQ 20V 403 A 1 
HETATM 28 C CBB 20V . . . F 3 87.823 85.52 91.968 1 183.16 ? CBB 20V 403 A 1 
HETATM 29 N NBJ 20V . . . F 3 86.914 85.817 93.053 0 182.92 ? NBJ 20V 403 A 1 
HETATM 30 O OAJ 20V . . . F 3 87.344 85.688 94.384 0 182.79 ? OAJ 20V 403 A 1 
HETATM 31 O OAI 20V . . . F 3 85.819 86.159 92.816 0 182.97 ? OAI 20V 403 A 1 
HETATM 32 C CAS 20V . . . F 3 89.022 86.249 91.733 1 182.75 ? CAS 20V 403 A 1 
HETATM 33 C CBI 20V . . . F 3 89.904 86.046 90.776 1 181.41 ? CBI 20V 403 A 1 
HETATM 34 C CBF 20V . . . F 3 91.027 86.858 90.689 1 182.4 ? CBF 20V 403 A 1 
HETATM 35 S SBL 20V . . . F 3 91.309 88.217 91.884 1 184.6 ? SBL 20V 403 A 1 
HETATM 36 O OAM 20V . . . F 3 90.161 88.54 92.792 1 187.52 ? OAM 20V 403 A 1 
HETATM 37 O OAE 20V . . . F 3 92.463 87.88 92.805 1 181.09 ? OAE 20V 403 A 1 
HETATM 38 O OAD 20V . . . F 3 91.675 89.493 91.152 1 179.83 ? OAD 20V 403 A 1 
HETATM 39 C CAP 20V . . . F 3 91.889 86.599 89.662 1 182.59 ? CAP 20V 403 A 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           39 
#