data_1GC3
#
_model_server_result.job_id            NvztMtmkkmzHCULgcp55qg 
_model_server_result.datetime_utc      '2024-11-02 05:23:24' 
_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          1gc3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":913}' 
#
_entry.id    1GC3 
#
_exptl.entry_id    1GC3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "PYRIDOXAL-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.53 
_cell.angle_gamma         90 
_cell.entry_id            1GC3 
_cell.length_a            81.5 
_cell.length_b            98.4 
_cell.length_c            187 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1GC3 
_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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L 1 1 
C,D,M,N,O,P 2 1 
E,F,Q,R,S,T 3 1 
G,H,U,V,W,X 4 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
? 3 K N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 S N N 
? 3 T N N 
? 3 V N N 
? 3 X 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
covale ? covale1 K C4A PLP . A PLP 413 1_555 I N TRP . A TRP 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? 
covale ? covale2 J N TRP . A TRP 914 1_555 L C4A PLP . B PLP 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 ? 
covale ? covale3 N C4A PLP . C PLP 1413 1_555 M N TRP . C TRP 1414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
covale ? covale4 P C4A PLP . D PLP 1913 1_555 O N TRP . D TRP 1914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.581 ? 
covale ? covale5 S C4A PLP . E PLP 2413 1_555 Q N TRP . E TRP 2414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? 
covale ? covale6 R N TRP . E TRP 2914 1_555 T C4A PLP . F PLP 2913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? 
covale ? covale7 V C4A PLP . G PLP 3413 1_555 U N TRP . G TRP 3414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.575 ? 
covale ? covale8 X C4A PLP . H PLP 3913 1_555 W N TRP . H TRP 3914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.538 ? 
#
_chem_comp.formula           'C8 H10 N O6 P' 
_chem_comp.formula_weight    247.142 
_chem_comp.id                PLP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "PYRIDOXAL-5'-PHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'VITAMIN B6 Phosphate' 
#
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 PLP doub 258 n y 
N1 C6 PLP sing 259 n y 
C2 C2A PLP sing 260 n n 
C2 C3 PLP sing 261 n y 
C2A H2A1 PLP sing 262 n n 
C2A H2A2 PLP sing 263 n n 
C2A H2A3 PLP sing 264 n n 
C3 O3 PLP sing 265 n n 
C3 C4 PLP doub 266 n y 
O3 HO3 PLP sing 267 n n 
C4 C4A PLP sing 268 n n 
C4 C5 PLP sing 269 n y 
C4A O4A PLP doub 270 n n 
C4A H4A PLP sing 271 n n 
C5 C6 PLP doub 272 n y 
C5 C5A PLP sing 273 n n 
C6 H6 PLP sing 274 n n 
C5A O4P PLP sing 275 n n 
C5A H5A1 PLP sing 276 n n 
C5A H5A2 PLP sing 277 n n 
O4P P PLP sing 278 n n 
P O1P PLP doub 279 n n 
P O2P PLP sing 280 n n 
P O3P PLP sing 281 n n 
O2P HOP2 PLP sing 282 n n 
O3P HOP3 PLP sing 283 n n 
#
_atom_sites.entry_id                     1GC3 
_atom_sites.fract_transf_matrix[1][1]    0.01227 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000328 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010163 
_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]    0.00535 
_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
I 2 TRP A 1 414 414 TRP TRP . 
J 2 TRP A 1 914 914 TRP TRP . 
K 3 PLP A 1 413 413 PLP PLP . 
L 3 PLP B 1 913 913 PLP PLP . 
M 2 TRP C 1 1414 1414 TRP TRP . 
N 3 PLP C 1 1413 1413 PLP PLP . 
O 2 TRP D 1 1914 1914 TRP TRP . 
P 3 PLP D 1 1913 1913 PLP PLP . 
Q 2 TRP E 1 2414 2414 TRP TRP . 
R 2 TRP E 1 2914 2914 TRP TRP . 
S 3 PLP E 1 2413 2413 PLP PLP . 
T 3 PLP F 1 2913 2913 PLP PLP . 
U 2 TRP G 1 3414 3414 TRP TRP . 
V 3 PLP G 1 3413 3413 PLP PLP . 
W 2 TRP H 1 3914 3914 TRP TRP . 
X 3 PLP H 1 3913 3913 PLP PLP . 
#
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 PLP . . . L 3 21.372 -1.681 79.652 1 2.47 ? N1 PLP 913 B 1 
HETATM 2 C C2 PLP . . . L 3 22.448 -0.974 79.281 1 4.85 ? C2 PLP 913 B 1 
HETATM 3 C C2A PLP . . . L 3 23.847 -1.508 79.693 1 2 ? C2A PLP 913 B 1 
HETATM 4 C C3 PLP . . . L 3 22.346 0.336 78.798 1 9.86 ? C3 PLP 913 B 1 
HETATM 5 O O3 PLP . . . L 3 23.491 0.893 78.176 1 6.92 ? O3 PLP 913 B 1 
HETATM 6 C C4 PLP . . . L 3 21.207 0.94 78.394 1 13.06 ? C4 PLP 913 B 1 
HETATM 7 C C4A PLP . . . L 3 21.309 1.822 76.986 1 20.48 ? C4A PLP 913 B 1 
HETATM 8 C C5 PLP . . . L 3 19.963 0.063 78.733 1 9.39 ? C5 PLP 913 B 1 
HETATM 9 C C6 PLP . . . L 3 20.132 -1.198 79.377 1 7.44 ? C6 PLP 913 B 1 
HETATM 10 C C5A PLP . . . L 3 18.488 0.396 78.369 1 7.25 ? C5A PLP 913 B 1 
HETATM 11 O O4P PLP . . . L 3 17.934 -0.388 77.29 1 7.5 ? O4P PLP 913 B 1 
HETATM 12 P P PLP . . . L 3 16.386 -0.348 76.816 1 11.08 ? P PLP 913 B 1 
HETATM 13 O O1P PLP . . . L 3 16.114 -1.574 76.027 1 10.97 ? O1P PLP 913 B 1 
HETATM 14 O O2P PLP . . . L 3 16.175 0.865 75.811 1 6.67 ? O2P PLP 913 B 1 
HETATM 15 O O3P PLP . . . L 3 15.571 -0.039 77.979 1 9.25 ? O3P PLP 913 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#