data_3DXV
#
_model_server_result.job_id            R2F_95kpF0HBllpjkoUxsg 
_model_server_result.datetime_utc      '2024-11-24 09:04:01' 
_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          3dxv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":450}' 
#
_entry.id    3DXV 
#
_exptl.entry_id    3DXV 
_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          103.22 
_cell.angle_gamma         90 
_cell.entry_id            3DXV 
_cell.length_a            56.547 
_cell.length_b            61.063 
_cell.length_c            105.227 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DXV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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 
_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 D 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 A NZ LYS 270 A LYS 267 1_555 C C4A PLP . A PLP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
covale ? covale2 B NZ LYS 270 B LYS 267 1_555 D C4A PLP . B PLP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
#
_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                     3DXV 
_atom_sites.fract_transf_matrix[1][1]    0.017684 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004156 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016377 
_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]    0.009762 
_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 1 450 450 PLP PLP . 
D 2 PLP B 1 450 450 PLP PLP . 
E 3 HOH A 1 451 1 HOH HOH . 
E 3 HOH A 2 452 3 HOH HOH . 
E 3 HOH A 3 453 4 HOH HOH . 
E 3 HOH A 4 454 5 HOH HOH . 
E 3 HOH A 5 455 7 HOH HOH . 
E 3 HOH A 6 456 10 HOH HOH . 
E 3 HOH A 7 457 12 HOH HOH . 
E 3 HOH A 8 458 13 HOH HOH . 
E 3 HOH A 9 459 15 HOH HOH . 
E 3 HOH A 10 460 17 HOH HOH . 
E 3 HOH A 11 461 19 HOH HOH . 
E 3 HOH A 12 462 20 HOH HOH . 
E 3 HOH A 13 463 22 HOH HOH . 
E 3 HOH A 14 464 23 HOH HOH . 
E 3 HOH A 15 465 24 HOH HOH . 
E 3 HOH A 16 466 25 HOH HOH . 
E 3 HOH A 17 467 29 HOH HOH . 
E 3 HOH A 18 468 31 HOH HOH . 
E 3 HOH A 19 469 32 HOH HOH . 
E 3 HOH A 20 470 34 HOH HOH . 
E 3 HOH A 21 471 36 HOH HOH . 
E 3 HOH A 22 472 37 HOH HOH . 
E 3 HOH A 23 473 38 HOH HOH . 
E 3 HOH A 24 474 41 HOH HOH . 
E 3 HOH A 25 475 43 HOH HOH . 
E 3 HOH A 26 476 48 HOH HOH . 
E 3 HOH A 27 477 50 HOH HOH . 
E 3 HOH A 28 478 51 HOH HOH . 
E 3 HOH A 29 479 52 HOH HOH . 
E 3 HOH A 30 480 53 HOH HOH . 
E 3 HOH A 31 481 54 HOH HOH . 
E 3 HOH A 32 482 57 HOH HOH . 
E 3 HOH A 33 483 62 HOH HOH . 
E 3 HOH A 34 484 63 HOH HOH . 
E 3 HOH A 35 485 66 HOH HOH . 
E 3 HOH A 36 486 67 HOH HOH . 
E 3 HOH A 37 487 69 HOH HOH . 
E 3 HOH A 38 488 71 HOH HOH . 
E 3 HOH A 39 489 72 HOH HOH . 
E 3 HOH A 40 490 73 HOH HOH . 
E 3 HOH A 41 491 74 HOH HOH . 
E 3 HOH A 42 492 75 HOH HOH . 
E 3 HOH A 43 493 77 HOH HOH . 
E 3 HOH A 44 494 78 HOH HOH . 
E 3 HOH A 45 495 79 HOH HOH . 
E 3 HOH A 46 496 83 HOH HOH . 
E 3 HOH A 47 497 84 HOH HOH . 
E 3 HOH A 48 498 85 HOH HOH . 
E 3 HOH A 49 499 86 HOH HOH . 
E 3 HOH A 50 500 88 HOH HOH . 
E 3 HOH A 51 501 89 HOH HOH . 
E 3 HOH A 52 502 90 HOH HOH . 
E 3 HOH A 53 503 91 HOH HOH . 
E 3 HOH A 54 504 92 HOH HOH . 
E 3 HOH A 55 505 95 HOH HOH . 
E 3 HOH A 56 506 100 HOH HOH . 
E 3 HOH A 57 507 103 HOH HOH . 
E 3 HOH A 58 508 104 HOH HOH . 
E 3 HOH A 59 509 106 HOH HOH . 
E 3 HOH A 60 510 109 HOH HOH . 
E 3 HOH A 61 511 110 HOH HOH . 
E 3 HOH A 62 512 112 HOH HOH . 
E 3 HOH A 63 513 115 HOH HOH . 
E 3 HOH A 64 514 116 HOH HOH . 
E 3 HOH A 65 515 117 HOH HOH . 
E 3 HOH A 66 516 119 HOH HOH . 
F 3 HOH B 1 451 2 HOH HOH . 
F 3 HOH B 2 452 6 HOH HOH . 
F 3 HOH B 3 453 8 HOH HOH . 
F 3 HOH B 4 454 9 HOH HOH . 
F 3 HOH B 5 455 11 HOH HOH . 
F 3 HOH B 6 456 14 HOH HOH . 
F 3 HOH B 7 457 16 HOH HOH . 
F 3 HOH B 8 458 18 HOH HOH . 
F 3 HOH B 9 459 21 HOH HOH . 
F 3 HOH B 10 460 26 HOH HOH . 
F 3 HOH B 11 461 27 HOH HOH . 
F 3 HOH B 12 462 28 HOH HOH . 
F 3 HOH B 13 463 30 HOH HOH . 
F 3 HOH B 14 464 33 HOH HOH . 
F 3 HOH B 15 465 35 HOH HOH . 
F 3 HOH B 16 466 39 HOH HOH . 
F 3 HOH B 17 467 40 HOH HOH . 
F 3 HOH B 18 468 42 HOH HOH . 
F 3 HOH B 19 469 44 HOH HOH . 
F 3 HOH B 20 470 45 HOH HOH . 
F 3 HOH B 21 471 46 HOH HOH . 
F 3 HOH B 22 472 47 HOH HOH . 
F 3 HOH B 23 473 49 HOH HOH . 
F 3 HOH B 24 474 55 HOH HOH . 
F 3 HOH B 25 475 56 HOH HOH . 
F 3 HOH B 26 476 58 HOH HOH . 
F 3 HOH B 27 477 59 HOH HOH . 
F 3 HOH B 28 478 60 HOH HOH . 
F 3 HOH B 29 479 61 HOH HOH . 
F 3 HOH B 30 480 64 HOH HOH . 
F 3 HOH B 31 481 65 HOH HOH . 
F 3 HOH B 32 482 68 HOH HOH . 
F 3 HOH B 33 483 70 HOH HOH . 
F 3 HOH B 34 484 76 HOH HOH . 
F 3 HOH B 35 485 80 HOH HOH . 
F 3 HOH B 36 486 81 HOH HOH . 
F 3 HOH B 37 487 82 HOH HOH . 
F 3 HOH B 38 488 87 HOH HOH . 
F 3 HOH B 39 489 93 HOH HOH . 
F 3 HOH B 40 490 94 HOH HOH . 
F 3 HOH B 41 491 96 HOH HOH . 
F 3 HOH B 42 492 97 HOH HOH . 
F 3 HOH B 43 493 98 HOH HOH . 
F 3 HOH B 44 494 99 HOH HOH . 
F 3 HOH B 45 495 101 HOH HOH . 
F 3 HOH B 46 496 102 HOH HOH . 
F 3 HOH B 47 497 105 HOH HOH . 
F 3 HOH B 48 498 107 HOH HOH . 
F 3 HOH B 49 499 108 HOH HOH . 
F 3 HOH B 50 500 111 HOH HOH . 
F 3 HOH B 51 501 113 HOH HOH . 
F 3 HOH B 52 502 114 HOH HOH . 
F 3 HOH B 53 503 118 HOH HOH . 
F 3 HOH B 54 504 120 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 . . . C 2 5.451 -5.248 34.813 1 21.43 ? N1 PLP 450 A 1 
HETATM 2 C C2 PLP . . . C 2 5.231 -3.897 35.022 1 21.15 ? C2 PLP 450 A 1 
HETATM 3 C C2A PLP . . . C 2 4.683 -3.465 36.347 1 21.17 ? C2A PLP 450 A 1 
HETATM 4 C C3 PLP . . . C 2 5.507 -2.966 34.004 1 22.48 ? C3 PLP 450 A 1 
HETATM 5 O O3 PLP . . . C 2 5.287 -1.769 34.221 1 22.08 ? O3 PLP 450 A 1 
HETATM 6 C C4 PLP . . . C 2 6.025 -3.41 32.767 1 21.23 ? C4 PLP 450 A 1 
HETATM 7 C C4A PLP . . . C 2 6.368 -2.495 31.599 1 22.06 ? C4A PLP 450 A 1 
HETATM 8 C C5 PLP . . . C 2 6.228 -4.792 32.593 1 21.15 ? C5 PLP 450 A 1 
HETATM 9 C C6 PLP . . . C 2 5.946 -5.699 33.61 1 20.45 ? C6 PLP 450 A 1 
HETATM 10 C C5A PLP . . . C 2 6.755 -5.353 31.309 1 20.69 ? C5A PLP 450 A 1 
HETATM 11 O O4P PLP . . . C 2 8 -4.864 30.779 1 21.53 ? O4P PLP 450 A 1 
HETATM 12 P P PLP . . . C 2 8.333 -4.902 29.214 1 20.81 ? P PLP 450 A 1 
HETATM 13 O O1P PLP . . . C 2 8.164 -6.332 28.881 1 22.49 ? O1P PLP 450 A 1 
HETATM 14 O O2P PLP . . . C 2 7.372 -4.013 28.526 1 20.19 ? O2P PLP 450 A 1 
HETATM 15 O O3P PLP . . . C 2 9.713 -4.399 29.199 1 20.08 ? O3P PLP 450 A 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           15 
#