data_1RV4
#
_model_server_result.job_id            jyo10c49aD5_tZdku6VGRw 
_model_server_result.datetime_utc      '2024-10-10 01:14:37' 
_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          1rv4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    1RV4 
#
_exptl.entry_id    1RV4 
_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            1RV4 
_cell.length_a            115.04 
_cell.length_b            115.04 
_cell.length_c            158.39 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RV4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 158.39 
#
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 F 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 256 A LYS 257 1_555 D C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? 
covale ? covale2 B NZ LYS 256 B LYS 257 1_555 F C4A PLP . B PLP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? 
#
_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                     1RV4 
_atom_sites.fract_transf_matrix[1][1]    0.008693 
_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]    0.008693 
_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]    0.006314 
_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 PO4 A 1 501 501 PO4 PO4 . 
D 3 PLP A 1 500 500 PLP PLP . 
E 2 PO4 B 1 601 601 PO4 PO4 . 
F 3 PLP B 1 600 600 PLP PLP . 
G 4 HOH A 1 511 511 HOH HOH . 
G 4 HOH A 2 512 512 HOH HOH . 
G 4 HOH A 3 514 514 HOH HOH . 
G 4 HOH A 4 515 515 HOH HOH . 
G 4 HOH A 5 516 516 HOH HOH . 
G 4 HOH A 6 517 517 HOH HOH . 
G 4 HOH A 7 518 518 HOH HOH . 
G 4 HOH A 8 519 519 HOH HOH . 
G 4 HOH A 9 520 520 HOH HOH . 
G 4 HOH A 10 521 521 HOH HOH . 
G 4 HOH A 11 522 522 HOH HOH . 
G 4 HOH A 12 523 523 HOH HOH . 
G 4 HOH A 13 524 524 HOH HOH . 
G 4 HOH A 14 526 526 HOH HOH . 
G 4 HOH A 15 527 527 HOH HOH . 
G 4 HOH A 16 528 528 HOH HOH . 
G 4 HOH A 17 529 529 HOH HOH . 
G 4 HOH A 18 530 530 HOH HOH . 
G 4 HOH A 19 531 531 HOH HOH . 
G 4 HOH A 20 532 532 HOH HOH . 
G 4 HOH A 21 533 533 HOH HOH . 
G 4 HOH A 22 534 534 HOH HOH . 
G 4 HOH A 23 535 535 HOH HOH . 
G 4 HOH A 24 536 536 HOH HOH . 
G 4 HOH A 25 537 537 HOH HOH . 
G 4 HOH A 26 538 538 HOH HOH . 
G 4 HOH A 27 539 539 HOH HOH . 
G 4 HOH A 28 541 541 HOH HOH . 
G 4 HOH A 29 542 542 HOH HOH . 
G 4 HOH A 30 543 543 HOH HOH . 
G 4 HOH A 31 544 544 HOH HOH . 
G 4 HOH A 32 545 545 HOH HOH . 
G 4 HOH A 33 546 546 HOH HOH . 
G 4 HOH A 34 547 547 HOH HOH . 
G 4 HOH A 35 548 548 HOH HOH . 
G 4 HOH A 36 549 549 HOH HOH . 
G 4 HOH A 37 550 550 HOH HOH . 
G 4 HOH A 38 552 552 HOH HOH . 
G 4 HOH A 39 613 613 HOH HOH . 
G 4 HOH A 40 625 625 HOH HOH . 
G 4 HOH A 41 641 641 HOH HOH . 
G 4 HOH A 42 651 651 HOH HOH . 
G 4 HOH A 43 655 655 HOH HOH . 
H 4 HOH B 1 513 513 HOH HOH . 
H 4 HOH B 2 525 525 HOH HOH . 
H 4 HOH B 3 540 540 HOH HOH . 
H 4 HOH B 4 551 551 HOH HOH . 
H 4 HOH B 5 612 612 HOH HOH . 
H 4 HOH B 6 614 614 HOH HOH . 
H 4 HOH B 7 615 615 HOH HOH . 
H 4 HOH B 8 616 616 HOH HOH . 
H 4 HOH B 9 617 617 HOH HOH . 
H 4 HOH B 10 618 618 HOH HOH . 
H 4 HOH B 11 619 619 HOH HOH . 
H 4 HOH B 12 620 620 HOH HOH . 
H 4 HOH B 13 621 621 HOH HOH . 
H 4 HOH B 14 622 622 HOH HOH . 
H 4 HOH B 15 623 623 HOH HOH . 
H 4 HOH B 16 624 624 HOH HOH . 
H 4 HOH B 17 626 626 HOH HOH . 
H 4 HOH B 18 627 627 HOH HOH . 
H 4 HOH B 19 628 628 HOH HOH . 
H 4 HOH B 20 629 629 HOH HOH . 
H 4 HOH B 21 630 630 HOH HOH . 
H 4 HOH B 22 631 631 HOH HOH . 
H 4 HOH B 23 632 632 HOH HOH . 
H 4 HOH B 24 633 633 HOH HOH . 
H 4 HOH B 25 634 634 HOH HOH . 
H 4 HOH B 26 635 635 HOH HOH . 
H 4 HOH B 27 636 636 HOH HOH . 
H 4 HOH B 28 637 637 HOH HOH . 
H 4 HOH B 29 638 638 HOH HOH . 
H 4 HOH B 30 639 639 HOH HOH . 
H 4 HOH B 31 640 640 HOH HOH . 
H 4 HOH B 32 642 642 HOH HOH . 
H 4 HOH B 33 643 643 HOH HOH . 
H 4 HOH B 34 644 644 HOH HOH . 
H 4 HOH B 35 645 645 HOH HOH . 
H 4 HOH B 36 646 646 HOH HOH . 
H 4 HOH B 37 647 647 HOH HOH . 
H 4 HOH B 38 648 648 HOH HOH . 
H 4 HOH B 39 649 649 HOH HOH . 
H 4 HOH B 40 650 650 HOH HOH . 
H 4 HOH B 41 652 652 HOH HOH . 
H 4 HOH B 42 653 653 HOH HOH . 
H 4 HOH B 43 654 654 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 . . . D 3 52.556 80.474 69.604 1 43.18 ? N1 PLP 500 A 1 
HETATM 2 C C2 PLP . . . D 3 53.1 81.773 69.579 1 45.74 ? C2 PLP 500 A 1 
HETATM 3 C C2A PLP . . . D 3 54.517 81.976 69.17 1 44.46 ? C2A PLP 500 A 1 
HETATM 4 C C3 PLP . . . D 3 52.223 82.915 69.972 1 46.27 ? C3 PLP 500 A 1 
HETATM 5 O O3 PLP . . . D 3 52.608 84.213 69.998 1 48.62 ? O3 PLP 500 A 1 
HETATM 6 C C4 PLP . . . D 3 50.761 82.588 70.384 1 48.42 ? C4 PLP 500 A 1 
HETATM 7 C C4A PLP . . . D 3 49.868 83.543 70.762 1 49.6 ? C4A PLP 500 A 1 
HETATM 8 C C5 PLP . . . D 3 50.311 81.172 70.379 1 47.27 ? C5 PLP 500 A 1 
HETATM 9 C C6 PLP . . . D 3 51.253 80.129 69.973 1 46.62 ? C6 PLP 500 A 1 
HETATM 10 C C5A PLP . . . D 3 48.898 80.718 70.814 1 47.66 ? C5A PLP 500 A 1 
HETATM 11 O O4P PLP . . . D 3 47.743 80.813 69.966 1 46.17 ? O4P PLP 500 A 1 
HETATM 12 P P PLP . . . D 3 46.44 80.326 70.311 1 44.79 ? P PLP 500 A 1 
HETATM 13 O O1P PLP . . . D 3 46.028 81.199 71.498 1 42.75 ? O1P PLP 500 A 1 
HETATM 14 O O2P PLP . . . D 3 45.625 80.637 69.175 1 44.49 ? O2P PLP 500 A 1 
HETATM 15 O O3P PLP . . . D 3 46.088 79.031 70.726 1 45.49 ? O3P PLP 500 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#