data_8VHH
#
_model_server_result.job_id            Vq-eL1ovf1gYoo1z0P1RDg 
_model_server_result.datetime_utc      '2024-12-02 05:32:08' 
_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          8vhh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":401}' 
#
_entry.id    8VHH 
#
_exptl.entry_id    8VHH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          2 
_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            8VHH 
_cell.length_a            165.698 
_cell.length_b            165.698 
_cell.length_c            83.061 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VHH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    'I 4' 
_symmetry.space_group_name_H-M     'I 4' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 G 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 OG SER 228 A SER 228 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.284 ? 
metalc ? metalc2 A O ALA 263 A ALA 263 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? 
metalc ? metalc3 A OG SER 265 A SER 265 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc4 A O TYR 301 A TYR 301 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? 
metalc ? metalc5 A O GLY 303 A GLY 303 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? 
metalc ? metalc6 D K K . A K 402 1_555 J O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? 
metalc ? metalc7 B O ALA 263 B ALA 263 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc8 B OG SER 265 B SER 265 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? 
metalc ? metalc9 B O TYR 301 B TYR 301 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc10 B O GLY 303 B GLY 303 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? 
metalc ? metalc11 H K K . B K 402 1_555 K O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? 
#
_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 260 n y 
N1 C6 PLP sing 261 n y 
C2 C2A PLP sing 262 n n 
C2 C3 PLP sing 263 n y 
C2A H2A1 PLP sing 264 n n 
C2A H2A2 PLP sing 265 n n 
C2A H2A3 PLP sing 266 n n 
C3 O3 PLP sing 267 n n 
C3 C4 PLP doub 268 n y 
O3 HO3 PLP sing 269 n n 
C4 C4A PLP sing 270 n n 
C4 C5 PLP sing 271 n y 
C4A O4A PLP doub 272 n n 
C4A H4A PLP sing 273 n n 
C5 C6 PLP doub 274 n y 
C5 C5A PLP sing 275 n n 
C6 H6 PLP sing 276 n n 
C5A O4P PLP sing 277 n n 
C5A H5A1 PLP sing 278 n n 
C5A H5A2 PLP sing 279 n n 
O4P P PLP sing 280 n n 
P O1P PLP doub 281 n n 
P O2P PLP sing 282 n n 
P O3P PLP sing 283 n n 
O2P HOP2 PLP sing 284 n n 
O3P HOP3 PLP sing 285 n n 
#
_atom_sites.entry_id                     8VHH 
_atom_sites.fract_transf_matrix[1][1]    0.006035 
_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]    0.006035 
_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]    0.012039 
_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
C 2 PLP A 1 401 401 PLP PLP . 
D 3 K A 1 402 1 K K . 
E 4 PO4 A 1 403 1 PO4 PO4 . 
F 4 PO4 A 1 404 3 PO4 PO4 . 
G 2 PLP B 1 401 401 PLP PLP . 
H 3 K B 1 402 2 K K . 
I 4 PO4 B 1 403 2 PO4 PO4 . 
J 5 HOH A 1 501 1 HOH HOH . 
J 5 HOH A 2 502 48 HOH HOH . 
J 5 HOH A 3 503 16 HOH HOH . 
J 5 HOH A 4 504 40 HOH HOH . 
J 5 HOH A 5 505 57 HOH HOH . 
J 5 HOH A 6 506 73 HOH HOH . 
J 5 HOH A 7 507 41 HOH HOH . 
J 5 HOH A 8 508 8 HOH HOH . 
J 5 HOH A 9 509 77 HOH HOH . 
J 5 HOH A 10 510 23 HOH HOH . 
J 5 HOH A 11 511 19 HOH HOH . 
J 5 HOH A 12 512 32 HOH HOH . 
J 5 HOH A 13 513 45 HOH HOH . 
J 5 HOH A 14 514 11 HOH HOH . 
J 5 HOH A 15 515 62 HOH HOH . 
J 5 HOH A 16 516 91 HOH HOH . 
J 5 HOH A 17 517 81 HOH HOH . 
J 5 HOH A 18 518 22 HOH HOH . 
J 5 HOH A 19 519 12 HOH HOH . 
J 5 HOH A 20 520 54 HOH HOH . 
J 5 HOH A 21 521 34 HOH HOH . 
J 5 HOH A 22 522 68 HOH HOH . 
J 5 HOH A 23 523 26 HOH HOH . 
J 5 HOH A 24 524 88 HOH HOH . 
J 5 HOH A 25 525 89 HOH HOH . 
J 5 HOH A 26 526 37 HOH HOH . 
J 5 HOH A 27 527 79 HOH HOH . 
J 5 HOH A 28 528 86 HOH HOH . 
J 5 HOH A 29 529 39 HOH HOH . 
J 5 HOH A 30 530 35 HOH HOH . 
J 5 HOH A 31 531 53 HOH HOH . 
J 5 HOH A 32 532 13 HOH HOH . 
J 5 HOH A 33 533 61 HOH HOH . 
J 5 HOH A 34 534 85 HOH HOH . 
J 5 HOH A 35 535 47 HOH HOH . 
J 5 HOH A 36 536 43 HOH HOH . 
J 5 HOH A 37 537 67 HOH HOH . 
J 5 HOH A 38 538 29 HOH HOH . 
J 5 HOH A 39 539 4 HOH HOH . 
J 5 HOH A 40 540 25 HOH HOH . 
J 5 HOH A 41 541 80 HOH HOH . 
J 5 HOH A 42 542 82 HOH HOH . 
J 5 HOH A 43 543 14 HOH HOH . 
J 5 HOH A 44 544 38 HOH HOH . 
J 5 HOH A 45 545 60 HOH HOH . 
J 5 HOH A 46 546 15 HOH HOH . 
J 5 HOH A 47 547 51 HOH HOH . 
J 5 HOH A 48 548 56 HOH HOH . 
J 5 HOH A 49 549 7 HOH HOH . 
J 5 HOH A 50 550 28 HOH HOH . 
J 5 HOH A 51 551 75 HOH HOH . 
J 5 HOH A 52 552 74 HOH HOH . 
J 5 HOH A 53 553 55 HOH HOH . 
J 5 HOH A 54 554 6 HOH HOH . 
J 5 HOH A 55 555 17 HOH HOH . 
J 5 HOH A 56 556 65 HOH HOH . 
J 5 HOH A 57 557 87 HOH HOH . 
J 5 HOH A 58 558 9 HOH HOH . 
J 5 HOH A 59 559 63 HOH HOH . 
J 5 HOH A 60 560 46 HOH HOH . 
J 5 HOH A 61 561 94 HOH HOH . 
J 5 HOH A 62 562 58 HOH HOH . 
J 5 HOH A 63 563 70 HOH HOH . 
J 5 HOH A 64 564 93 HOH HOH . 
J 5 HOH A 65 565 64 HOH HOH . 
K 5 HOH B 1 501 42 HOH HOH . 
K 5 HOH B 2 502 92 HOH HOH . 
K 5 HOH B 3 503 2 HOH HOH . 
K 5 HOH B 4 504 27 HOH HOH . 
K 5 HOH B 5 505 84 HOH HOH . 
K 5 HOH B 6 506 24 HOH HOH . 
K 5 HOH B 7 507 36 HOH HOH . 
K 5 HOH B 8 508 10 HOH HOH . 
K 5 HOH B 9 509 59 HOH HOH . 
K 5 HOH B 10 510 3 HOH HOH . 
K 5 HOH B 11 511 72 HOH HOH . 
K 5 HOH B 12 512 66 HOH HOH . 
K 5 HOH B 13 513 33 HOH HOH . 
K 5 HOH B 14 514 78 HOH HOH . 
K 5 HOH B 15 515 21 HOH HOH . 
K 5 HOH B 16 516 18 HOH HOH . 
K 5 HOH B 17 517 30 HOH HOH . 
K 5 HOH B 18 518 31 HOH HOH . 
K 5 HOH B 19 519 76 HOH HOH . 
K 5 HOH B 20 520 49 HOH HOH . 
K 5 HOH B 21 521 20 HOH HOH . 
K 5 HOH B 22 522 50 HOH HOH . 
K 5 HOH B 23 523 5 HOH HOH . 
K 5 HOH B 24 524 44 HOH HOH . 
K 5 HOH B 25 525 83 HOH HOH . 
K 5 HOH B 26 526 71 HOH HOH . 
K 5 HOH B 27 527 52 HOH HOH . 
K 5 HOH B 28 528 69 HOH HOH . 
K 5 HOH B 29 529 90 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 . . . G 2 -0.867 51.43 -9.915 1 59.04 ? N1 PLP 401 B 1 
HETATM 2 C C2 PLP . . . G 2 -0.321 50.403 -9.173 1 57.24 ? C2 PLP 401 B 1 
HETATM 3 C C2A PLP . . . G 2 1.155 50.151 -9.206 1 48.61 ? C2A PLP 401 B 1 
HETATM 4 C C3 PLP . . . G 2 -1.136 49.596 -8.39 1 59.39 ? C3 PLP 401 B 1 
HETATM 5 O O3 PLP . . . G 2 -0.586 48.578 -7.657 1 70.22 ? O3 PLP 401 B 1 
HETATM 6 C C4 PLP . . . G 2 -2.509 49.814 -8.348 1 60.92 ? C4 PLP 401 B 1 
HETATM 7 C C4A PLP . . . G 2 -3.328 48.955 -7.425 1 59.69 ? C4A PLP 401 B 1 
HETATM 8 O O4A PLP . . . G 2 -4.169 49.42 -6.657 1 61.95 ? O4A PLP 401 B 1 
HETATM 9 C C5 PLP . . . G 2 -3.058 50.854 -9.101 1 54.69 ? C5 PLP 401 B 1 
HETATM 10 C C6 PLP . . . G 2 -2.228 51.656 -9.879 1 50.08 ? C6 PLP 401 B 1 
HETATM 11 C C5A PLP . . . G 2 -4.539 51.156 -9.099 1 55.78 ? C5A PLP 401 B 1 
HETATM 12 O O4P PLP . . . G 2 -4.733 52.117 -8.087 1 54.94 ? O4P PLP 401 B 1 
HETATM 13 P P PLP . . . G 2 -5.584 53.452 -8.355 1 46.52 ? P PLP 401 B 1 
HETATM 14 O O1P PLP . . . G 2 -6.381 53.312 -9.631 1 47.86 ? O1P PLP 401 B 1 
HETATM 15 O O2P PLP . . . G 2 -4.629 54.614 -8.477 1 49.08 ? O2P PLP 401 B 1 
HETATM 16 O O3P PLP . . . G 2 -6.52 53.667 -7.194 1 44.23 ? O3P PLP 401 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           16 
#