data_3WGB
#
_model_server_result.job_id            E9lSDgky06qB1XeI_YRZyQ 
_model_server_result.datetime_utc      '2024-11-05 00:38:52' 
_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          3wgb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    3WGB 
#
_exptl.entry_id    3WGB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              306.209 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          113.64 
_cell.angle_gamma         90 
_cell.entry_id            3WGB 
_cell.length_a            82.474 
_cell.length_b            95.85 
_cell.length_c            94.884 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3WGB 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,G,H,I,J,K,L,M 
_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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C10 H15 N2 O7 P' 
_chem_comp.formula_weight    306.209 
_chem_comp.id                PLG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE 
#
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 PLG doub 260 n y 
N1 C6 PLG sing 261 n y 
C2 C2A PLG sing 262 n n 
C2 C3 PLG sing 263 n y 
C2A H2A1 PLG sing 264 n n 
C2A H2A2 PLG sing 265 n n 
C2A H2A3 PLG sing 266 n n 
C3 O3 PLG sing 267 n n 
C3 C4 PLG doub 268 n y 
O3 HO3 PLG sing 269 n n 
C4 C4A PLG sing 270 n n 
C4 C5 PLG sing 271 n y 
C4A N PLG sing 272 n n 
C4A H4A1 PLG sing 273 n n 
C4A H4A2 PLG sing 274 n n 
C5 C6 PLG doub 275 n y 
C5 C5A PLG sing 276 n n 
C6 H6 PLG sing 277 n n 
C5A OP4 PLG sing 278 n n 
C5A H5A1 PLG sing 279 n n 
C5A H5A2 PLG sing 280 n n 
OP4 P PLG sing 281 n n 
P OP1 PLG doub 282 n n 
P OP2 PLG sing 283 n n 
P OP3 PLG sing 284 n n 
OP2 HOP2 PLG sing 285 n n 
OP3 HOP3 PLG sing 286 n n 
C O PLG doub 287 n n 
C OXT PLG sing 288 n n 
C CA PLG sing 289 n n 
OXT HXT PLG sing 290 n n 
CA N PLG sing 291 n n 
CA HA2 PLG sing 292 n n 
CA HA1 PLG sing 293 n n 
N H PLG sing 294 n n 
#
_atom_sites.entry_id                     3WGB 
_atom_sites.fract_transf_matrix[1][1]    0.012125 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005307 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010433 
_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]    0.011505 
_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
E 2 PLG A 1 401 6205 PLG PLG . 
F 2 PLG B 1 401 6205 PLG PLG . 
G 2 PLG C 1 401 6205 PLG PLG . 
H 2 PLG D 1 401 6205 PLG PLG . 
I 3 GLY D 1 402 339 GLY GLY . 
J 4 HOH A 1 501 339 HOH HOH . 
J 4 HOH A 2 502 340 HOH HOH . 
J 4 HOH A 3 503 341 HOH HOH . 
J 4 HOH A 4 504 342 HOH HOH . 
J 4 HOH A 5 505 343 HOH HOH . 
J 4 HOH A 6 506 344 HOH HOH . 
J 4 HOH A 7 507 345 HOH HOH . 
J 4 HOH A 8 508 346 HOH HOH . 
J 4 HOH A 9 509 347 HOH HOH . 
J 4 HOH A 10 510 348 HOH HOH . 
J 4 HOH A 11 511 349 HOH HOH . 
J 4 HOH A 12 512 350 HOH HOH . 
J 4 HOH A 13 513 351 HOH HOH . 
J 4 HOH A 14 514 352 HOH HOH . 
J 4 HOH A 15 515 353 HOH HOH . 
J 4 HOH A 16 516 354 HOH HOH . 
J 4 HOH A 17 517 355 HOH HOH . 
J 4 HOH A 18 518 356 HOH HOH . 
J 4 HOH A 19 519 357 HOH HOH . 
J 4 HOH A 20 520 358 HOH HOH . 
J 4 HOH A 21 521 359 HOH HOH . 
J 4 HOH A 22 522 360 HOH HOH . 
J 4 HOH A 23 523 361 HOH HOH . 
J 4 HOH A 24 524 362 HOH HOH . 
J 4 HOH A 25 525 363 HOH HOH . 
J 4 HOH A 26 526 364 HOH HOH . 
J 4 HOH A 27 527 365 HOH HOH . 
J 4 HOH A 28 528 366 HOH HOH . 
J 4 HOH A 29 529 367 HOH HOH . 
J 4 HOH A 30 530 368 HOH HOH . 
J 4 HOH A 31 531 369 HOH HOH . 
J 4 HOH A 32 532 370 HOH HOH . 
J 4 HOH A 33 533 371 HOH HOH . 
J 4 HOH A 34 534 372 HOH HOH . 
J 4 HOH A 35 535 373 HOH HOH . 
J 4 HOH A 36 536 374 HOH HOH . 
J 4 HOH A 37 537 375 HOH HOH . 
J 4 HOH A 38 538 376 HOH HOH . 
J 4 HOH A 39 539 377 HOH HOH . 
J 4 HOH A 40 540 378 HOH HOH . 
J 4 HOH A 41 541 379 HOH HOH . 
K 4 HOH B 1 501 339 HOH HOH . 
K 4 HOH B 2 502 340 HOH HOH . 
K 4 HOH B 3 503 341 HOH HOH . 
K 4 HOH B 4 504 342 HOH HOH . 
K 4 HOH B 5 505 343 HOH HOH . 
K 4 HOH B 6 506 344 HOH HOH . 
K 4 HOH B 7 507 345 HOH HOH . 
K 4 HOH B 8 508 346 HOH HOH . 
K 4 HOH B 9 509 347 HOH HOH . 
K 4 HOH B 10 510 348 HOH HOH . 
K 4 HOH B 11 511 349 HOH HOH . 
K 4 HOH B 12 512 350 HOH HOH . 
K 4 HOH B 13 513 351 HOH HOH . 
K 4 HOH B 14 514 352 HOH HOH . 
K 4 HOH B 15 515 353 HOH HOH . 
K 4 HOH B 16 516 354 HOH HOH . 
K 4 HOH B 17 517 355 HOH HOH . 
K 4 HOH B 18 518 356 HOH HOH . 
K 4 HOH B 19 519 357 HOH HOH . 
K 4 HOH B 20 520 358 HOH HOH . 
K 4 HOH B 21 521 359 HOH HOH . 
K 4 HOH B 22 522 360 HOH HOH . 
K 4 HOH B 23 523 361 HOH HOH . 
K 4 HOH B 24 524 362 HOH HOH . 
K 4 HOH B 25 525 363 HOH HOH . 
K 4 HOH B 26 526 364 HOH HOH . 
K 4 HOH B 27 527 365 HOH HOH . 
K 4 HOH B 28 528 366 HOH HOH . 
K 4 HOH B 29 529 367 HOH HOH . 
K 4 HOH B 30 530 368 HOH HOH . 
K 4 HOH B 31 531 369 HOH HOH . 
K 4 HOH B 32 532 370 HOH HOH . 
K 4 HOH B 33 533 371 HOH HOH . 
K 4 HOH B 34 534 372 HOH HOH . 
K 4 HOH B 35 535 373 HOH HOH . 
K 4 HOH B 36 536 374 HOH HOH . 
K 4 HOH B 37 537 375 HOH HOH . 
K 4 HOH B 38 538 376 HOH HOH . 
K 4 HOH B 39 539 377 HOH HOH . 
K 4 HOH B 40 540 378 HOH HOH . 
K 4 HOH B 41 541 379 HOH HOH . 
K 4 HOH B 42 542 380 HOH HOH . 
K 4 HOH B 43 543 381 HOH HOH . 
K 4 HOH B 44 544 382 HOH HOH . 
K 4 HOH B 45 545 383 HOH HOH . 
K 4 HOH B 46 546 384 HOH HOH . 
K 4 HOH B 47 547 385 HOH HOH . 
L 4 HOH C 1 501 339 HOH HOH . 
L 4 HOH C 2 502 341 HOH HOH . 
L 4 HOH C 3 503 342 HOH HOH . 
L 4 HOH C 4 504 343 HOH HOH . 
L 4 HOH C 5 505 344 HOH HOH . 
L 4 HOH C 6 506 345 HOH HOH . 
L 4 HOH C 7 507 346 HOH HOH . 
L 4 HOH C 8 508 347 HOH HOH . 
L 4 HOH C 9 509 348 HOH HOH . 
L 4 HOH C 10 510 349 HOH HOH . 
L 4 HOH C 11 511 350 HOH HOH . 
L 4 HOH C 12 512 351 HOH HOH . 
L 4 HOH C 13 513 352 HOH HOH . 
L 4 HOH C 14 514 353 HOH HOH . 
L 4 HOH C 15 515 354 HOH HOH . 
L 4 HOH C 16 516 355 HOH HOH . 
L 4 HOH C 17 517 356 HOH HOH . 
L 4 HOH C 18 518 357 HOH HOH . 
L 4 HOH C 19 519 358 HOH HOH . 
L 4 HOH C 20 520 359 HOH HOH . 
L 4 HOH C 21 521 360 HOH HOH . 
L 4 HOH C 22 522 361 HOH HOH . 
L 4 HOH C 23 523 362 HOH HOH . 
L 4 HOH C 24 524 363 HOH HOH . 
L 4 HOH C 25 525 364 HOH HOH . 
L 4 HOH C 26 526 365 HOH HOH . 
L 4 HOH C 27 527 366 HOH HOH . 
L 4 HOH C 28 528 367 HOH HOH . 
L 4 HOH C 29 529 368 HOH HOH . 
L 4 HOH C 30 530 369 HOH HOH . 
L 4 HOH C 31 531 370 HOH HOH . 
L 4 HOH C 32 532 371 HOH HOH . 
L 4 HOH C 33 533 372 HOH HOH . 
L 4 HOH C 34 534 373 HOH HOH . 
L 4 HOH C 35 535 374 HOH HOH . 
L 4 HOH C 36 536 375 HOH HOH . 
L 4 HOH C 37 537 376 HOH HOH . 
L 4 HOH C 38 538 377 HOH HOH . 
L 4 HOH C 39 539 378 HOH HOH . 
L 4 HOH C 40 540 380 HOH HOH . 
L 4 HOH C 41 541 381 HOH HOH . 
L 4 HOH C 42 542 382 HOH HOH . 
L 4 HOH C 43 543 383 HOH HOH . 
L 4 HOH C 44 544 384 HOH HOH . 
L 4 HOH C 45 545 385 HOH HOH . 
L 4 HOH C 46 546 386 HOH HOH . 
L 4 HOH C 47 547 387 HOH HOH . 
L 4 HOH C 48 548 388 HOH HOH . 
M 4 HOH D 1 501 340 HOH HOH . 
M 4 HOH D 2 502 341 HOH HOH . 
M 4 HOH D 3 503 342 HOH HOH . 
M 4 HOH D 4 504 343 HOH HOH . 
M 4 HOH D 5 505 344 HOH HOH . 
M 4 HOH D 6 506 345 HOH HOH . 
M 4 HOH D 7 507 346 HOH HOH . 
M 4 HOH D 8 508 347 HOH HOH . 
M 4 HOH D 9 509 348 HOH HOH . 
M 4 HOH D 10 510 349 HOH HOH . 
M 4 HOH D 11 511 350 HOH HOH . 
M 4 HOH D 12 512 351 HOH HOH . 
M 4 HOH D 13 513 352 HOH HOH . 
M 4 HOH D 14 514 353 HOH HOH . 
M 4 HOH D 15 515 354 HOH HOH . 
M 4 HOH D 16 516 355 HOH HOH . 
M 4 HOH D 17 517 356 HOH HOH . 
M 4 HOH D 18 518 357 HOH HOH . 
M 4 HOH D 19 519 358 HOH HOH . 
M 4 HOH D 20 520 359 HOH HOH . 
M 4 HOH D 21 521 360 HOH HOH . 
M 4 HOH D 22 522 361 HOH HOH . 
M 4 HOH D 23 523 362 HOH HOH . 
M 4 HOH D 24 524 363 HOH HOH . 
M 4 HOH D 25 525 364 HOH HOH . 
M 4 HOH D 26 526 365 HOH HOH . 
M 4 HOH D 27 527 366 HOH HOH . 
M 4 HOH D 28 528 367 HOH HOH . 
M 4 HOH D 29 529 368 HOH HOH . 
M 4 HOH D 30 530 369 HOH HOH . 
M 4 HOH D 31 531 370 HOH HOH . 
M 4 HOH D 32 532 371 HOH HOH . 
M 4 HOH D 33 533 379 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 PLG . . . F 2 58.766 -9.208 14.48 1 22.53 ? N1 PLG 401 B 1 
HETATM 2 C C2 PLG . . . F 2 59.969 -8.772 14.03 1 22.73 ? C2 PLG 401 B 1 
HETATM 3 C C2A PLG . . . F 2 61.212 -9.573 14.308 1 22.13 ? C2A PLG 401 B 1 
HETATM 4 C C3 PLG . . . F 2 60.065 -7.505 13.26 1 23.34 ? C3 PLG 401 B 1 
HETATM 5 O O3 PLG . . . F 2 61.272 -7.063 12.81 1 23.65 ? O3 PLG 401 B 1 
HETATM 6 C C4 PLG . . . F 2 58.809 -6.748 13.01 1 23.92 ? C4 PLG 401 B 1 
HETATM 7 C C4A PLG . . . F 2 58.827 -5.442 12.235 1 24.6 ? C4A PLG 401 B 1 
HETATM 8 C C5 PLG . . . F 2 57.551 -7.345 13.554 1 23.05 ? C5 PLG 401 B 1 
HETATM 9 C C6 PLG . . . F 2 57.615 -8.544 14.267 1 22.61 ? C6 PLG 401 B 1 
HETATM 10 C C5A PLG . . . F 2 56.199 -6.683 13.398 1 22.97 ? C5A PLG 401 B 1 
HETATM 11 O OP4 PLG . . . F 2 55.665 -6.756 12.082 1 22.5 ? OP4 PLG 401 B 1 
HETATM 12 P P PLG . . . F 2 54.53 -5.702 11.64 1 22.48 ? P PLG 401 B 1 
HETATM 13 O OP1 PLG . . . F 2 54.034 -6.245 10.323 1 22.93 ? OP1 PLG 401 B 1 
HETATM 14 O OP2 PLG . . . F 2 53.513 -5.735 12.755 1 22.22 ? OP2 PLG 401 B 1 
HETATM 15 O OP3 PLG . . . F 2 55.259 -4.386 11.524 1 22.65 ? OP3 PLG 401 B 1 
HETATM 16 C C PLG . . . F 2 60.657 -2.978 10.936 1 25.24 ? C PLG 401 B 1 
HETATM 17 O O PLG . . . F 2 59.473 -2.574 10.924 1 25.39 ? O PLG 401 B 1 
HETATM 18 O OXT PLG . . . F 2 61.578 -2.398 10.322 1 25.27 ? OXT PLG 401 B 1 
HETATM 19 C CA PLG . . . F 2 60.989 -4.221 11.727 1 25.06 ? CA PLG 401 B 1 
HETATM 20 N N PLG . . . F 2 59.932 -4.594 12.655 1 24.79 ? N PLG 401 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#