data_1RVU
#
_model_server_result.job_id            GX0isAH6yZDQkKrYzqsxUg 
_model_server_result.datetime_utc      '2024-11-28 21:59:08' 
_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          1rvu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    1RVU 
#
_exptl.entry_id    1RVU 
_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            1RVU 
_cell.length_a            114.65 
_cell.length_b            114.65 
_cell.length_c            156.79 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RVU 
_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 
_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 0 156.79 
#
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 E 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 C C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale2 B NZ LYS 256 B LYS 257 1_555 E C4A PLP . B PLP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
#
_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                     1RVU 
_atom_sites.fract_transf_matrix[1][1]    0.008722 
_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]    0.008722 
_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]    0.006378 
_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 1 500 500 PLP PLP . 
D 3 PO4 B 1 601 601 PO4 PO4 . 
E 2 PLP B 1 600 600 PLP PLP . 
F 4 HOH A 1 506 506 HOH HOH . 
F 4 HOH A 2 511 511 HOH HOH . 
F 4 HOH A 3 512 512 HOH HOH . 
F 4 HOH A 4 514 514 HOH HOH . 
F 4 HOH A 5 515 515 HOH HOH . 
F 4 HOH A 6 516 516 HOH HOH . 
F 4 HOH A 7 517 517 HOH HOH . 
F 4 HOH A 8 518 518 HOH HOH . 
F 4 HOH A 9 519 519 HOH HOH . 
F 4 HOH A 10 520 520 HOH HOH . 
F 4 HOH A 11 521 521 HOH HOH . 
F 4 HOH A 12 522 522 HOH HOH . 
F 4 HOH A 13 523 523 HOH HOH . 
F 4 HOH A 14 524 524 HOH HOH . 
F 4 HOH A 15 526 526 HOH HOH . 
F 4 HOH A 16 527 527 HOH HOH . 
F 4 HOH A 17 528 528 HOH HOH . 
F 4 HOH A 18 529 529 HOH HOH . 
F 4 HOH A 19 530 530 HOH HOH . 
F 4 HOH A 20 531 531 HOH HOH . 
F 4 HOH A 21 532 532 HOH HOH . 
F 4 HOH A 22 533 533 HOH HOH . 
F 4 HOH A 23 534 534 HOH HOH . 
F 4 HOH A 24 535 535 HOH HOH . 
F 4 HOH A 25 536 536 HOH HOH . 
F 4 HOH A 26 537 537 HOH HOH . 
F 4 HOH A 27 538 538 HOH HOH . 
F 4 HOH A 28 539 539 HOH HOH . 
F 4 HOH A 29 541 541 HOH HOH . 
F 4 HOH A 30 542 542 HOH HOH . 
F 4 HOH A 31 543 543 HOH HOH . 
F 4 HOH A 32 544 544 HOH HOH . 
F 4 HOH A 33 545 545 HOH HOH . 
F 4 HOH A 34 546 546 HOH HOH . 
F 4 HOH A 35 547 547 HOH HOH . 
F 4 HOH A 36 548 548 HOH HOH . 
F 4 HOH A 37 549 549 HOH HOH . 
F 4 HOH A 38 550 550 HOH HOH . 
F 4 HOH A 39 551 551 HOH HOH . 
F 4 HOH A 40 552 552 HOH HOH . 
F 4 HOH A 41 553 553 HOH HOH . 
F 4 HOH A 42 557 557 HOH HOH . 
F 4 HOH A 43 560 560 HOH HOH . 
F 4 HOH A 44 561 561 HOH HOH . 
F 4 HOH A 45 562 562 HOH HOH . 
F 4 HOH A 46 564 564 HOH HOH . 
F 4 HOH A 47 613 613 HOH HOH . 
F 4 HOH A 48 615 615 HOH HOH . 
F 4 HOH A 49 625 625 HOH HOH . 
F 4 HOH A 50 655 655 HOH HOH . 
F 4 HOH A 51 656 656 HOH HOH . 
F 4 HOH A 52 657 657 HOH HOH . 
F 4 HOH A 53 659 659 HOH HOH . 
F 4 HOH A 54 660 660 HOH HOH . 
G 4 HOH B 1 505 505 HOH HOH . 
G 4 HOH B 2 507 507 HOH HOH . 
G 4 HOH B 3 513 513 HOH HOH . 
G 4 HOH B 4 525 525 HOH HOH . 
G 4 HOH B 5 540 540 HOH HOH . 
G 4 HOH B 6 556 556 HOH HOH . 
G 4 HOH B 7 611 611 HOH HOH . 
G 4 HOH B 8 612 612 HOH HOH . 
G 4 HOH B 9 614 614 HOH HOH . 
G 4 HOH B 10 616 616 HOH HOH . 
G 4 HOH B 11 617 617 HOH HOH . 
G 4 HOH B 12 618 618 HOH HOH . 
G 4 HOH B 13 619 619 HOH HOH . 
G 4 HOH B 14 620 620 HOH HOH . 
G 4 HOH B 15 621 621 HOH HOH . 
G 4 HOH B 16 622 622 HOH HOH . 
G 4 HOH B 17 623 623 HOH HOH . 
G 4 HOH B 18 624 624 HOH HOH . 
G 4 HOH B 19 626 626 HOH HOH . 
G 4 HOH B 20 627 627 HOH HOH . 
G 4 HOH B 21 628 628 HOH HOH . 
G 4 HOH B 22 629 629 HOH HOH . 
G 4 HOH B 23 630 630 HOH HOH . 
G 4 HOH B 24 631 631 HOH HOH . 
G 4 HOH B 25 632 632 HOH HOH . 
G 4 HOH B 26 633 633 HOH HOH . 
G 4 HOH B 27 634 634 HOH HOH . 
G 4 HOH B 28 635 635 HOH HOH . 
G 4 HOH B 29 636 636 HOH HOH . 
G 4 HOH B 30 637 637 HOH HOH . 
G 4 HOH B 31 638 638 HOH HOH . 
G 4 HOH B 32 639 639 HOH HOH . 
G 4 HOH B 33 640 640 HOH HOH . 
G 4 HOH B 34 641 641 HOH HOH . 
G 4 HOH B 35 642 642 HOH HOH . 
G 4 HOH B 36 643 643 HOH HOH . 
G 4 HOH B 37 644 644 HOH HOH . 
G 4 HOH B 38 645 645 HOH HOH . 
G 4 HOH B 39 646 646 HOH HOH . 
G 4 HOH B 40 647 647 HOH HOH . 
G 4 HOH B 41 648 648 HOH HOH . 
G 4 HOH B 42 649 649 HOH HOH . 
G 4 HOH B 43 650 650 HOH HOH . 
G 4 HOH B 44 651 651 HOH HOH . 
G 4 HOH B 45 652 652 HOH HOH . 
G 4 HOH B 46 653 653 HOH HOH . 
G 4 HOH B 47 654 654 HOH HOH . 
G 4 HOH B 48 658 658 HOH HOH . 
G 4 HOH B 49 661 661 HOH HOH . 
G 4 HOH B 50 663 663 HOH HOH . 
G 4 HOH B 51 694 694 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 52.559 80.165 69.017 1 24.23 ? N1 PLP 500 A 1 
HETATM 2 C C2 PLP . . . C 2 53.047 81.487 68.95 1 26.79 ? C2 PLP 500 A 1 
HETATM 3 C C2A PLP . . . C 2 54.49 81.736 68.617 1 25.51 ? C2A PLP 500 A 1 
HETATM 4 C C3 PLP . . . C 2 52.089 82.602 69.219 1 27.32 ? C3 PLP 500 A 1 
HETATM 5 O O3 PLP . . . C 2 52.396 83.915 69.195 1 29.67 ? O3 PLP 500 A 1 
HETATM 6 C C4 PLP . . . C 2 50.632 82.226 69.555 1 29.47 ? C4 PLP 500 A 1 
HETATM 7 C C4A PLP . . . C 2 49.702 83.141 69.816 1 30.65 ? C4A PLP 500 A 1 
HETATM 8 C C5 PLP . . . C 2 50.241 80.79 69.607 1 28.32 ? C5 PLP 500 A 1 
HETATM 9 C C6 PLP . . . C 2 51.25 79.777 69.323 1 27.67 ? C6 PLP 500 A 1 
HETATM 10 C C5A PLP . . . C 2 48.83 80.285 69.977 1 28.71 ? C5A PLP 500 A 1 
HETATM 11 O O4P PLP . . . C 2 47.691 80.423 69.124 1 27.22 ? O4P PLP 500 A 1 
HETATM 12 P P PLP . . . C 2 46.367 80.025 69.492 1 25.84 ? P PLP 500 A 1 
HETATM 13 O O1P PLP . . . C 2 46.011 80.956 70.63 1 23.8 ? O1P PLP 500 A 1 
HETATM 14 O O2P PLP . . . C 2 45.544 80.321 68.357 1 25.54 ? O2P PLP 500 A 1 
HETATM 15 O O3P PLP . . . C 2 45.971 78.786 69.994 1 26.54 ? O3P PLP 500 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#