data_3DYD
#
_model_server_result.job_id            JlWhcS6N4YpsehxnbO61rA 
_model_server_result.datetime_utc      '2024-10-18 16:23:10' 
_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          3dyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3DYD 
#
_exptl.entry_id    3DYD 
_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          106.18 
_cell.angle_gamma         90 
_cell.entry_id            3DYD 
_cell.length_a            154.42 
_cell.length_b            91.59 
_cell.length_c            75.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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 263 A LYS 280 1_555 C C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.684 ? 
covale ? covale2 B NZ LYS 263 B LYS 280 1_555 D C4A PLP . B PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? 
#
_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                     3DYD 
_atom_sites.fract_transf_matrix[1][1]    0.006476 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001879 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010918 
_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]    0.013779 
_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 2 PLP B 1 500 500 PLP PLP . 
E 3 HOH A 1 501 2 HOH HOH . 
E 3 HOH A 2 502 5 HOH HOH . 
E 3 HOH A 3 503 8 HOH HOH . 
E 3 HOH A 4 504 12 HOH HOH . 
E 3 HOH A 5 505 13 HOH HOH . 
E 3 HOH A 6 506 14 HOH HOH . 
E 3 HOH A 7 507 20 HOH HOH . 
E 3 HOH A 8 508 21 HOH HOH . 
E 3 HOH A 9 509 22 HOH HOH . 
E 3 HOH A 10 510 25 HOH HOH . 
E 3 HOH A 11 511 28 HOH HOH . 
E 3 HOH A 12 512 30 HOH HOH . 
E 3 HOH A 13 513 31 HOH HOH . 
E 3 HOH A 14 514 34 HOH HOH . 
E 3 HOH A 15 515 36 HOH HOH . 
E 3 HOH A 16 516 44 HOH HOH . 
E 3 HOH A 17 517 45 HOH HOH . 
E 3 HOH A 18 518 47 HOH HOH . 
E 3 HOH A 19 519 49 HOH HOH . 
E 3 HOH A 20 520 50 HOH HOH . 
E 3 HOH A 21 521 54 HOH HOH . 
E 3 HOH A 22 522 57 HOH HOH . 
E 3 HOH A 23 523 59 HOH HOH . 
E 3 HOH A 24 524 63 HOH HOH . 
E 3 HOH A 25 525 64 HOH HOH . 
E 3 HOH A 26 526 67 HOH HOH . 
E 3 HOH A 27 527 68 HOH HOH . 
E 3 HOH A 28 528 69 HOH HOH . 
E 3 HOH A 29 529 70 HOH HOH . 
E 3 HOH A 30 530 73 HOH HOH . 
E 3 HOH A 31 531 76 HOH HOH . 
E 3 HOH A 32 532 78 HOH HOH . 
E 3 HOH A 33 533 82 HOH HOH . 
E 3 HOH A 34 534 83 HOH HOH . 
E 3 HOH A 35 535 84 HOH HOH . 
E 3 HOH A 36 536 90 HOH HOH . 
E 3 HOH A 37 537 92 HOH HOH . 
E 3 HOH A 38 538 93 HOH HOH . 
E 3 HOH A 39 539 94 HOH HOH . 
E 3 HOH A 40 540 95 HOH HOH . 
E 3 HOH A 41 541 98 HOH HOH . 
E 3 HOH A 42 542 99 HOH HOH . 
E 3 HOH A 43 543 100 HOH HOH . 
E 3 HOH A 44 544 104 HOH HOH . 
E 3 HOH A 45 545 111 HOH HOH . 
E 3 HOH A 46 546 118 HOH HOH . 
E 3 HOH A 47 547 119 HOH HOH . 
E 3 HOH A 48 548 121 HOH HOH . 
E 3 HOH A 49 549 122 HOH HOH . 
E 3 HOH A 50 550 126 HOH HOH . 
E 3 HOH A 51 551 128 HOH HOH . 
E 3 HOH A 52 552 130 HOH HOH . 
E 3 HOH A 53 553 131 HOH HOH . 
E 3 HOH A 54 554 132 HOH HOH . 
E 3 HOH A 55 555 135 HOH HOH . 
E 3 HOH A 56 556 137 HOH HOH . 
E 3 HOH A 57 557 141 HOH HOH . 
E 3 HOH A 58 558 143 HOH HOH . 
E 3 HOH A 59 559 146 HOH HOH . 
E 3 HOH A 60 560 147 HOH HOH . 
E 3 HOH A 61 561 148 HOH HOH . 
E 3 HOH A 62 562 150 HOH HOH . 
E 3 HOH A 63 563 151 HOH HOH . 
E 3 HOH A 64 564 152 HOH HOH . 
E 3 HOH A 65 565 155 HOH HOH . 
E 3 HOH A 66 566 156 HOH HOH . 
E 3 HOH A 67 567 157 HOH HOH . 
E 3 HOH A 68 568 158 HOH HOH . 
E 3 HOH A 69 569 159 HOH HOH . 
E 3 HOH A 70 570 163 HOH HOH . 
E 3 HOH A 71 571 167 HOH HOH . 
E 3 HOH A 72 572 169 HOH HOH . 
E 3 HOH A 73 573 171 HOH HOH . 
E 3 HOH A 74 574 173 HOH HOH . 
E 3 HOH A 75 575 174 HOH HOH . 
E 3 HOH A 76 576 175 HOH HOH . 
E 3 HOH A 77 577 176 HOH HOH . 
E 3 HOH A 78 578 177 HOH HOH . 
E 3 HOH A 79 579 180 HOH HOH . 
E 3 HOH A 80 580 186 HOH HOH . 
E 3 HOH A 81 581 187 HOH HOH . 
E 3 HOH A 82 582 188 HOH HOH . 
E 3 HOH A 83 583 189 HOH HOH . 
E 3 HOH A 84 584 195 HOH HOH . 
E 3 HOH A 85 585 196 HOH HOH . 
E 3 HOH A 86 586 197 HOH HOH . 
E 3 HOH A 87 587 200 HOH HOH . 
E 3 HOH A 88 588 201 HOH HOH . 
E 3 HOH A 89 589 204 HOH HOH . 
E 3 HOH A 90 590 205 HOH HOH . 
F 3 HOH B 1 501 1 HOH HOH . 
F 3 HOH B 2 502 3 HOH HOH . 
F 3 HOH B 3 503 4 HOH HOH . 
F 3 HOH B 4 504 6 HOH HOH . 
F 3 HOH B 5 505 7 HOH HOH . 
F 3 HOH B 6 506 9 HOH HOH . 
F 3 HOH B 7 507 10 HOH HOH . 
F 3 HOH B 8 508 11 HOH HOH . 
F 3 HOH B 9 509 15 HOH HOH . 
F 3 HOH B 10 510 16 HOH HOH . 
F 3 HOH B 11 511 17 HOH HOH . 
F 3 HOH B 12 512 18 HOH HOH . 
F 3 HOH B 13 513 19 HOH HOH . 
F 3 HOH B 14 514 23 HOH HOH . 
F 3 HOH B 15 515 24 HOH HOH . 
F 3 HOH B 16 516 26 HOH HOH . 
F 3 HOH B 17 517 27 HOH HOH . 
F 3 HOH B 18 518 29 HOH HOH . 
F 3 HOH B 19 519 32 HOH HOH . 
F 3 HOH B 20 520 33 HOH HOH . 
F 3 HOH B 21 521 35 HOH HOH . 
F 3 HOH B 22 522 37 HOH HOH . 
F 3 HOH B 23 523 38 HOH HOH . 
F 3 HOH B 24 524 39 HOH HOH . 
F 3 HOH B 25 525 40 HOH HOH . 
F 3 HOH B 26 526 41 HOH HOH . 
F 3 HOH B 27 527 42 HOH HOH . 
F 3 HOH B 28 528 43 HOH HOH . 
F 3 HOH B 29 529 46 HOH HOH . 
F 3 HOH B 30 530 48 HOH HOH . 
F 3 HOH B 31 531 51 HOH HOH . 
F 3 HOH B 32 532 52 HOH HOH . 
F 3 HOH B 33 533 53 HOH HOH . 
F 3 HOH B 34 534 55 HOH HOH . 
F 3 HOH B 35 535 56 HOH HOH . 
F 3 HOH B 36 536 58 HOH HOH . 
F 3 HOH B 37 537 60 HOH HOH . 
F 3 HOH B 38 538 61 HOH HOH . 
F 3 HOH B 39 539 62 HOH HOH . 
F 3 HOH B 40 540 65 HOH HOH . 
F 3 HOH B 41 541 66 HOH HOH . 
F 3 HOH B 42 542 71 HOH HOH . 
F 3 HOH B 43 543 72 HOH HOH . 
F 3 HOH B 44 544 74 HOH HOH . 
F 3 HOH B 45 545 75 HOH HOH . 
F 3 HOH B 46 546 77 HOH HOH . 
F 3 HOH B 47 547 79 HOH HOH . 
F 3 HOH B 48 548 80 HOH HOH . 
F 3 HOH B 49 549 81 HOH HOH . 
F 3 HOH B 50 550 85 HOH HOH . 
F 3 HOH B 51 551 86 HOH HOH . 
F 3 HOH B 52 552 87 HOH HOH . 
F 3 HOH B 53 553 88 HOH HOH . 
F 3 HOH B 54 554 89 HOH HOH . 
F 3 HOH B 55 555 91 HOH HOH . 
F 3 HOH B 56 556 96 HOH HOH . 
F 3 HOH B 57 557 97 HOH HOH . 
F 3 HOH B 58 558 101 HOH HOH . 
F 3 HOH B 59 559 102 HOH HOH . 
F 3 HOH B 60 560 103 HOH HOH . 
F 3 HOH B 61 561 105 HOH HOH . 
F 3 HOH B 62 562 106 HOH HOH . 
F 3 HOH B 63 563 107 HOH HOH . 
F 3 HOH B 64 564 108 HOH HOH . 
F 3 HOH B 65 565 109 HOH HOH . 
F 3 HOH B 66 566 110 HOH HOH . 
F 3 HOH B 67 567 112 HOH HOH . 
F 3 HOH B 68 568 113 HOH HOH . 
F 3 HOH B 69 569 114 HOH HOH . 
F 3 HOH B 70 570 115 HOH HOH . 
F 3 HOH B 71 571 116 HOH HOH . 
F 3 HOH B 72 572 117 HOH HOH . 
F 3 HOH B 73 573 120 HOH HOH . 
F 3 HOH B 74 574 123 HOH HOH . 
F 3 HOH B 75 575 124 HOH HOH . 
F 3 HOH B 76 576 125 HOH HOH . 
F 3 HOH B 77 577 127 HOH HOH . 
F 3 HOH B 78 578 129 HOH HOH . 
F 3 HOH B 79 579 133 HOH HOH . 
F 3 HOH B 80 580 134 HOH HOH . 
F 3 HOH B 81 581 136 HOH HOH . 
F 3 HOH B 82 582 138 HOH HOH . 
F 3 HOH B 83 583 139 HOH HOH . 
F 3 HOH B 84 584 140 HOH HOH . 
F 3 HOH B 85 585 142 HOH HOH . 
F 3 HOH B 86 586 144 HOH HOH . 
F 3 HOH B 87 587 145 HOH HOH . 
F 3 HOH B 88 588 149 HOH HOH . 
F 3 HOH B 89 589 153 HOH HOH . 
F 3 HOH B 90 590 154 HOH HOH . 
F 3 HOH B 91 591 160 HOH HOH . 
F 3 HOH B 92 592 161 HOH HOH . 
F 3 HOH B 93 593 162 HOH HOH . 
F 3 HOH B 94 594 164 HOH HOH . 
F 3 HOH B 95 595 165 HOH HOH . 
F 3 HOH B 96 596 166 HOH HOH . 
F 3 HOH B 97 597 168 HOH HOH . 
F 3 HOH B 98 598 170 HOH HOH . 
F 3 HOH B 99 599 172 HOH HOH . 
F 3 HOH B 100 600 178 HOH HOH . 
F 3 HOH B 101 601 179 HOH HOH . 
F 3 HOH B 102 602 181 HOH HOH . 
F 3 HOH B 103 603 182 HOH HOH . 
F 3 HOH B 104 604 183 HOH HOH . 
F 3 HOH B 105 605 184 HOH HOH . 
F 3 HOH B 106 606 185 HOH HOH . 
F 3 HOH B 107 607 190 HOH HOH . 
F 3 HOH B 108 608 191 HOH HOH . 
F 3 HOH B 109 609 192 HOH HOH . 
F 3 HOH B 110 610 193 HOH HOH . 
F 3 HOH B 111 611 194 HOH HOH . 
F 3 HOH B 112 612 198 HOH HOH . 
F 3 HOH B 113 613 199 HOH HOH . 
F 3 HOH B 114 614 202 HOH HOH . 
F 3 HOH B 115 615 203 HOH HOH . 
F 3 HOH B 116 616 206 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 23.592 89.066 14.251 1 8.26 ? N1 PLP 500 A 1 
HETATM 2 C C2 PLP . . . C 2 22.406 88.622 13.701 1 8.02 ? C2 PLP 500 A 1 
HETATM 3 C C2A PLP . . . C 2 21.101 89.178 14.188 1 7.9 ? C2A PLP 500 A 1 
HETATM 4 C C3 PLP . . . C 2 22.42 87.661 12.697 1 7.7 ? C3 PLP 500 A 1 
HETATM 5 O O3 PLP . . . C 2 21.241 87.144 12.229 1 7.6 ? O3 PLP 500 A 1 
HETATM 6 C C4 PLP . . . C 2 23.631 87.147 12.247 1 8.44 ? C4 PLP 500 A 1 
HETATM 7 C C4A PLP . . . C 2 23.658 86.216 11.071 1 7.33 ? C4A PLP 500 A 1 
HETATM 8 C C5 PLP . . . C 2 24.822 87.597 12.804 1 9.31 ? C5 PLP 500 A 1 
HETATM 9 C C6 PLP . . . C 2 24.797 88.558 13.807 1 9.42 ? C6 PLP 500 A 1 
HETATM 10 C C5A PLP . . . C 2 26.122 86.913 12.45 1 9.79 ? C5A PLP 500 A 1 
HETATM 11 O O4P PLP . . . C 2 26.648 87.484 11.273 1 10.91 ? O4P PLP 500 A 1 
HETATM 12 P P PLP . . . C 2 28.036 86.949 10.656 1 11.75 ? P PLP 500 A 1 
HETATM 13 O O1P PLP . . . C 2 28.652 88.019 9.786 1 11.91 ? O1P PLP 500 A 1 
HETATM 14 O O2P PLP . . . C 2 27.783 85.709 9.833 1 11.13 ? O2P PLP 500 A 1 
HETATM 15 O O3P PLP . . . C 2 28.969 86.621 11.796 1 11.58 ? O3P PLP 500 A 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#