data_2ZR8
#
_model_server_result.job_id            gZvETvESaKvlcyRo2SIq5g 
_model_server_result.datetime_utc      '2025-01-03 07:29:58' 
_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          2zr8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":350}' 
#
_entry.id    2ZR8 
#
_exptl.entry_id    2ZR8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              320.236 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          101.73 
_cell.angle_gamma         90 
_cell.entry_id            2ZR8 
_cell.length_a            59.54 
_cell.length_b            72.88 
_cell.length_c            64.81 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ZR8 
_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 
_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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 46.364128 0 63.45654 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 57 A LYS 57 1_555 B CB PDD . A PDD 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? 
metalc ? metalc1 A OE2 GLU 208 A GLU 208 1_555 D MG MG . A MG 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc2 A O GLY 212 A GLY 212 1_555 D MG MG . A MG 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc3 A OD1 ASP 214 A ASP 214 1_555 D MG MG . A MG 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc4 D MG MG . A MG 360 1_555 E O HOH . A HOH 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc5 D MG MG . A MG 360 1_555 E O HOH . A HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc6 D MG MG . A MG 360 1_555 E O HOH . A HOH 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
#
_chem_comp.formula           'C11 H17 N2 O7 P' 
_chem_comp.formula_weight    320.236 
_chem_comp.id                PDD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" 
_chem_comp.type              'd-peptide linking' 
_chem_comp.pdbx_synonyms     ? 
#
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
N C4A PDD sing 237 n n 
N CA PDD sing 238 n n 
N H PDD sing 239 n n 
N1 C2 PDD doub 240 n y 
N1 C6 PDD sing 241 n y 
C2 C2A PDD sing 242 n n 
C2 C3 PDD sing 243 n y 
C2A H2A1 PDD sing 244 n n 
C2A H2A2 PDD sing 245 n n 
C2A H2A3 PDD sing 246 n n 
C3 O3A PDD sing 247 n n 
C3 C4 PDD doub 248 n y 
O3A HO3 PDD sing 249 n n 
C4 C4A PDD sing 250 n n 
C4 C5 PDD sing 251 n y 
C4A H4A1 PDD sing 252 n n 
C4A H4A2 PDD sing 253 n n 
C5 C5A PDD sing 254 n n 
C5 C6 PDD doub 255 n y 
C5A OP4 PDD sing 256 n n 
C5A H5A1 PDD sing 257 n n 
C5A H5A2 PDD sing 258 n n 
OP4 P PDD sing 259 n n 
P OP1 PDD doub 260 n n 
P OP2 PDD sing 261 n n 
P OP3 PDD sing 262 n n 
OP2 HOP2 PDD sing 263 n n 
OP3 HOP3 PDD sing 264 n n 
C6 H6 PDD sing 265 n n 
CA CB PDD sing 266 n n 
CA C PDD sing 267 n n 
CA HA PDD sing 268 n n 
CB HB1 PDD sing 269 n n 
CB HB2 PDD sing 270 n n 
CB HB3 PDD sing 271 n n 
C O PDD doub 272 n n 
C OXT PDD sing 273 n n 
OXT HXT PDD sing 274 n n 
#
_atom_sites.entry_id                     2ZR8 
_atom_sites.fract_transf_matrix[1][1]    0.016795 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003487 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013721 
_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]    0.015759 
_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
B 2 PDD A 1 350 350 PDD PDD . 
C 3 SER A 1 370 370 SER SER . 
D 4 MG A 1 360 360 MG MG . 
E 5 HOH A 1 371 1 HOH HOH . 
E 5 HOH A 2 372 2 HOH HOH . 
E 5 HOH A 3 373 3 HOH HOH . 
E 5 HOH A 4 374 4 HOH HOH . 
E 5 HOH A 5 375 5 HOH HOH . 
E 5 HOH A 6 376 6 HOH HOH . 
E 5 HOH A 7 377 7 HOH HOH . 
E 5 HOH A 8 378 8 HOH HOH . 
E 5 HOH A 9 379 9 HOH HOH . 
E 5 HOH A 10 380 10 HOH HOH . 
E 5 HOH A 11 381 11 HOH HOH . 
E 5 HOH A 12 382 12 HOH HOH . 
E 5 HOH A 13 383 13 HOH HOH . 
E 5 HOH A 14 384 14 HOH HOH . 
E 5 HOH A 15 385 15 HOH HOH . 
E 5 HOH A 16 386 16 HOH HOH . 
E 5 HOH A 17 387 17 HOH HOH . 
E 5 HOH A 18 388 18 HOH HOH . 
E 5 HOH A 19 389 19 HOH HOH . 
E 5 HOH A 20 390 20 HOH HOH . 
E 5 HOH A 21 391 21 HOH HOH . 
E 5 HOH A 22 392 22 HOH HOH . 
E 5 HOH A 23 393 23 HOH HOH . 
E 5 HOH A 24 394 24 HOH HOH . 
E 5 HOH A 25 395 25 HOH HOH . 
E 5 HOH A 26 396 26 HOH HOH . 
E 5 HOH A 27 397 27 HOH HOH . 
E 5 HOH A 28 398 28 HOH HOH . 
E 5 HOH A 29 399 29 HOH HOH . 
E 5 HOH A 30 400 30 HOH HOH . 
E 5 HOH A 31 401 31 HOH HOH . 
E 5 HOH A 32 402 32 HOH HOH . 
E 5 HOH A 33 403 33 HOH HOH . 
E 5 HOH A 34 404 34 HOH HOH . 
E 5 HOH A 35 405 35 HOH HOH . 
E 5 HOH A 36 406 36 HOH HOH . 
E 5 HOH A 37 407 37 HOH HOH . 
E 5 HOH A 38 408 38 HOH HOH . 
E 5 HOH A 39 409 39 HOH HOH . 
E 5 HOH A 40 410 40 HOH HOH . 
E 5 HOH A 41 411 41 HOH HOH . 
E 5 HOH A 42 412 42 HOH HOH . 
E 5 HOH A 43 413 43 HOH HOH . 
E 5 HOH A 44 414 44 HOH HOH . 
E 5 HOH A 45 415 45 HOH HOH . 
E 5 HOH A 46 416 46 HOH HOH . 
E 5 HOH A 47 417 47 HOH HOH . 
E 5 HOH A 48 418 48 HOH HOH . 
E 5 HOH A 49 419 49 HOH HOH . 
E 5 HOH A 50 420 50 HOH HOH . 
E 5 HOH A 51 421 51 HOH HOH . 
E 5 HOH A 52 422 52 HOH HOH . 
E 5 HOH A 53 423 53 HOH HOH . 
E 5 HOH A 54 424 54 HOH HOH . 
E 5 HOH A 55 425 55 HOH HOH . 
E 5 HOH A 56 426 56 HOH HOH . 
E 5 HOH A 57 427 57 HOH HOH . 
E 5 HOH A 58 428 58 HOH HOH . 
E 5 HOH A 59 429 59 HOH HOH . 
E 5 HOH A 60 430 60 HOH HOH . 
E 5 HOH A 61 431 61 HOH HOH . 
E 5 HOH A 62 432 62 HOH HOH . 
E 5 HOH A 63 433 63 HOH HOH . 
E 5 HOH A 64 434 64 HOH HOH . 
E 5 HOH A 65 435 65 HOH HOH . 
E 5 HOH A 66 436 66 HOH HOH . 
E 5 HOH A 67 437 67 HOH HOH . 
E 5 HOH A 68 438 68 HOH HOH . 
E 5 HOH A 69 439 69 HOH HOH . 
E 5 HOH A 70 440 70 HOH HOH . 
E 5 HOH A 71 441 71 HOH HOH . 
E 5 HOH A 72 442 72 HOH HOH . 
E 5 HOH A 73 443 73 HOH HOH . 
E 5 HOH A 74 444 74 HOH HOH . 
E 5 HOH A 75 445 75 HOH HOH . 
E 5 HOH A 76 446 76 HOH HOH . 
E 5 HOH A 77 447 77 HOH HOH . 
E 5 HOH A 78 448 78 HOH HOH . 
E 5 HOH A 79 449 79 HOH HOH . 
E 5 HOH A 80 450 80 HOH HOH . 
E 5 HOH A 81 451 81 HOH HOH . 
E 5 HOH A 82 452 82 HOH HOH . 
E 5 HOH A 83 453 83 HOH HOH . 
E 5 HOH A 84 454 84 HOH HOH . 
E 5 HOH A 85 455 85 HOH HOH . 
E 5 HOH A 86 456 86 HOH HOH . 
E 5 HOH A 87 457 87 HOH HOH . 
E 5 HOH A 88 458 88 HOH HOH . 
E 5 HOH A 89 459 89 HOH HOH . 
E 5 HOH A 90 460 90 HOH HOH . 
E 5 HOH A 91 461 91 HOH HOH . 
E 5 HOH A 92 462 92 HOH HOH . 
E 5 HOH A 93 463 93 HOH HOH . 
E 5 HOH A 94 464 94 HOH HOH . 
E 5 HOH A 95 465 95 HOH HOH . 
E 5 HOH A 96 466 96 HOH HOH . 
E 5 HOH A 97 467 97 HOH HOH . 
E 5 HOH A 98 468 98 HOH HOH . 
E 5 HOH A 99 469 99 HOH HOH . 
E 5 HOH A 100 470 100 HOH HOH . 
E 5 HOH A 101 471 101 HOH HOH . 
E 5 HOH A 102 472 102 HOH HOH . 
E 5 HOH A 103 473 103 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 N PDD . . . B 2 12.01 -3.315 15.109 1 19.9 ? N PDD 350 A 1 
HETATM 2 N N1 PDD . . . B 2 17.026 -2.925 16.875 1 16.88 ? N1 PDD 350 A 1 
HETATM 3 C C2 PDD . . . B 2 15.982 -3.438 17.684 1 17.44 ? C2 PDD 350 A 1 
HETATM 4 C C2A PDD . . . B 2 16.224 -3.725 19.124 1 15.49 ? C2A PDD 350 A 1 
HETATM 5 C C3 PDD . . . B 2 14.66 -3.671 17.041 1 17.38 ? C3 PDD 350 A 1 
HETATM 6 O O3A PDD . . . B 2 13.543 -4.154 17.642 1 17.32 ? O3A PDD 350 A 1 
HETATM 7 C C4 PDD . . . B 2 14.547 -3.333 15.554 1 18.36 ? C4 PDD 350 A 1 
HETATM 8 C C4A PDD . . . B 2 13.259 -3.521 14.785 1 16.12 ? C4A PDD 350 A 1 
HETATM 9 C C5 PDD . . . B 2 15.685 -2.808 14.821 1 17.2 ? C5 PDD 350 A 1 
HETATM 10 C C5A PDD . . . B 2 15.597 -2.462 13.333 1 17.53 ? C5A PDD 350 A 1 
HETATM 11 O OP4 PDD . . . B 2 14.759 -1.348 12.938 1 15.4 ? OP4 PDD 350 A 1 
HETATM 12 P P PDD . . . B 2 14.288 -1.129 11.616 1 17.8 ? P PDD 350 A 1 
HETATM 13 O OP1 PDD . . . B 2 13.339 -2.284 11.373 1 13.01 ? OP1 PDD 350 A 1 
HETATM 14 O OP2 PDD . . . B 2 13.534 0.078 11.67 1 14.21 ? OP2 PDD 350 A 1 
HETATM 15 O OP3 PDD . . . B 2 15.063 -1.111 10.461 1 13.78 ? OP3 PDD 350 A 1 
HETATM 16 C C6 PDD . . . B 2 16.948 -2.607 15.518 1 16.7 ? C6 PDD 350 A 1 
HETATM 17 C CA PDD . . . B 2 10.764 -3.495 14.331 1 20.38 ? CA PDD 350 A 1 
HETATM 18 C CB PDD . . . B 2 10.309 -2.213 13.699 1 20.31 ? CB PDD 350 A 1 
HETATM 19 C C PDD . . . B 2 9.579 -3.993 15.276 1 20.23 ? C PDD 350 A 1 
HETATM 20 O O PDD . . . B 2 9.759 -4.163 16.477 1 21.26 ? O PDD 350 A 1 
HETATM 21 O OXT PDD . . . B 2 8.439 -4.221 14.827 1 21.51 ? OXT PDD 350 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           21 
#