data_4EB7
#
_model_server_result.job_id            CCDs8pV8G3yJqF5ew-aN2Q 
_model_server_result.datetime_utc      '2025-02-20 15:35:54' 
_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          4eb7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    4EB7 
#
_exptl.entry_id    4EB7 
_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    2 
_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            4EB7 
_cell.length_a            75.469 
_cell.length_b            96.129 
_cell.length_c            152.793 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4EB7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,N 
_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    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 D N N 
? 3 H 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 C SG CYS 58 C CYS 58 1_555 J FE1 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc2 C NE2 HIS 101 C HIS 101 1_555 J FE2 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? 
metalc ? metalc3 C SG CYS 102 C CYS 102 1_555 J FE1 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc4 J FE2 FES . C FES 201 1_555 K S2 FES . C FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
#
_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 310 n y 
N1 C6 PLP sing 311 n y 
C2 C2A PLP sing 312 n n 
C2 C3 PLP sing 313 n y 
C2A H2A1 PLP sing 314 n n 
C2A H2A2 PLP sing 315 n n 
C2A H2A3 PLP sing 316 n n 
C3 O3 PLP sing 317 n n 
C3 C4 PLP doub 318 n y 
O3 HO3 PLP sing 319 n n 
C4 C4A PLP sing 320 n n 
C4 C5 PLP sing 321 n y 
C4A O4A PLP doub 322 n n 
C4A H4A PLP sing 323 n n 
C5 C6 PLP doub 324 n y 
C5 C5A PLP sing 325 n n 
C6 H6 PLP sing 326 n n 
C5A O4P PLP sing 327 n n 
C5A H5A1 PLP sing 328 n n 
C5A H5A2 PLP sing 329 n n 
O4P P PLP sing 330 n n 
P O1P PLP doub 331 n n 
P O2P PLP sing 332 n n 
P O3P PLP sing 333 n n 
O2P HOP2 PLP sing 334 n n 
O3P HOP3 PLP sing 335 n n 
#
_atom_sites.entry_id                     4EB7 
_atom_sites.fract_transf_matrix[1][1]    0.01325 
_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]    0.010403 
_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]    0.006545 
_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 3 PLP A 1 401 1 PLP PLP . 
E 4 GOL A 1 402 3 GOL GOL . 
F 4 GOL A 1 403 4 GOL GOL . 
G 5 EPE A 1 404 6 EPE EPE . 
H 3 PLP B 1 401 2 PLP PLP . 
I 4 GOL B 1 402 5 GOL GOL . 
J 6 FES C 1 201 7 FES FES . 
K 6 FES C 1 202 8 FES H2S . 
L 7 HOH A 1 501 1 HOH HOH . 
L 7 HOH A 2 502 2 HOH HOH . 
L 7 HOH A 3 503 3 HOH HOH . 
L 7 HOH A 4 504 4 HOH HOH . 
L 7 HOH A 5 505 5 HOH HOH . 
L 7 HOH A 6 506 6 HOH HOH . 
L 7 HOH A 7 507 7 HOH HOH . 
L 7 HOH A 8 508 8 HOH HOH . 
L 7 HOH A 9 509 9 HOH HOH . 
L 7 HOH A 10 510 10 HOH HOH . 
L 7 HOH A 11 511 11 HOH HOH . 
L 7 HOH A 12 512 12 HOH HOH . 
L 7 HOH A 13 513 13 HOH HOH . 
L 7 HOH A 14 514 14 HOH HOH . 
L 7 HOH A 15 515 15 HOH HOH . 
L 7 HOH A 16 516 23 HOH HOH . 
L 7 HOH A 17 517 24 HOH HOH . 
L 7 HOH A 18 518 29 HOH HOH . 
L 7 HOH A 19 519 30 HOH HOH . 
L 7 HOH A 20 520 34 HOH HOH . 
L 7 HOH A 21 521 35 HOH HOH . 
L 7 HOH A 22 522 36 HOH HOH . 
L 7 HOH A 23 523 37 HOH HOH . 
L 7 HOH A 24 524 40 HOH HOH . 
L 7 HOH A 25 525 46 HOH HOH . 
M 7 HOH B 1 501 16 HOH HOH . 
M 7 HOH B 2 502 17 HOH HOH . 
M 7 HOH B 3 503 18 HOH HOH . 
M 7 HOH B 4 504 19 HOH HOH . 
M 7 HOH B 5 505 20 HOH HOH . 
M 7 HOH B 6 506 21 HOH HOH . 
M 7 HOH B 7 507 22 HOH HOH . 
M 7 HOH B 8 508 31 HOH HOH . 
M 7 HOH B 9 509 33 HOH HOH . 
M 7 HOH B 10 510 38 HOH HOH . 
M 7 HOH B 11 511 39 HOH HOH . 
M 7 HOH B 12 512 42 HOH HOH . 
M 7 HOH B 13 513 43 HOH HOH . 
M 7 HOH B 14 514 44 HOH HOH . 
M 7 HOH B 15 515 45 HOH HOH . 
N 7 HOH C 1 301 25 HOH HOH . 
N 7 HOH C 2 302 26 HOH HOH . 
N 7 HOH C 3 303 27 HOH HOH . 
N 7 HOH C 4 304 28 HOH HOH . 
N 7 HOH C 5 305 32 HOH HOH . 
N 7 HOH C 6 306 41 HOH HOH . 
N 7 HOH C 7 307 47 HOH HOH . 
N 7 HOH C 8 308 48 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 PLP . . . H 3 -1.062 19.122 -31.148 0.7 49.32 ? N1 PLP 401 B 1 
HETATM 2 C C2 PLP . . . H 3 -1.734 18.993 -32.309 0.7 50.05 ? C2 PLP 401 B 1 
HETATM 3 C C2A PLP . . . H 3 -1 19.207 -33.603 0.7 50.12 ? C2A PLP 401 B 1 
HETATM 4 C C3 PLP . . . H 3 -3.082 18.664 -32.304 0.7 50.33 ? C3 PLP 401 B 1 
HETATM 5 O O3 PLP . . . H 3 -3.759 18.517 -33.481 0.7 50.45 ? O3 PLP 401 B 1 
HETATM 6 C C4 PLP . . . H 3 -3.726 18.474 -31.091 0.7 50.46 ? C4 PLP 401 B 1 
HETATM 7 C C4A PLP . . . H 3 -5.167 18.105 -31.091 0.7 52.23 ? C4A PLP 401 B 1 
HETATM 8 O O4A PLP . . . H 3 -5.963 18.729 -30.405 0.7 54.09 ? O4A PLP 401 B 1 
HETATM 9 C C5 PLP . . . H 3 -3.004 18.615 -29.909 0.7 47.82 ? C5 PLP 401 B 1 
HETATM 10 C C6 PLP . . . H 3 -1.668 18.95 -29.966 0.7 48.47 ? C6 PLP 401 B 1 
HETATM 11 C C5A PLP . . . H 3 -3.611 18.421 -28.542 0.7 46.98 ? C5A PLP 401 B 1 
HETATM 12 O O4P PLP . . . H 3 -4.162 17.111 -28.29 0.7 44.12 ? O4P PLP 401 B 1 
HETATM 13 P P PLP . . . H 3 -5.027 16.957 -26.936 0.7 44.57 ? P PLP 401 B 1 
HETATM 14 O O1P PLP . . . H 3 -5.734 15.632 -26.958 0.7 43.41 ? O1P PLP 401 B 1 
HETATM 15 O O2P PLP . . . H 3 -3.959 17.041 -25.856 0.7 43.9 ? O2P PLP 401 B 1 
HETATM 16 O O3P PLP . . . H 3 -6.003 18.142 -26.989 0.7 41.68 ? O3P PLP 401 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#