data_4WML
#
_model_server_result.job_id            IiHybEg3NDX47jyZKXmNrQ 
_model_server_result.datetime_utc      '2024-10-13 02:26:17' 
_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          4wml 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    4WML 
#
_exptl.entry_id    4WML 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              388.097 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            4WML 
_cell.length_a            61.56 
_cell.length_b            61.56 
_cell.length_c            132.49 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WML 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 B MG MG . A MG 301 1_555 C O1 PPC . A PPC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc2 B MG MG . A MG 301 1_555 C O2B PPC . A PPC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? 
metalc ? metalc3 B MG MG . A MG 301 1_555 C O2 PPC . A PPC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc4 B MG MG . A MG 301 1_555 C O3 PPC . A PPC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc5 B MG MG . A MG 301 1_555 D O HOH . A HOH 456 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc6 B MG MG . A MG 301 1_555 D O HOH . A HOH 457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
#
_chem_comp.formula           'C6 H15 O13 P3' 
_chem_comp.formula_weight    388.097 
_chem_comp.id                PPC 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     '5-PHOSPHORIBOSYL-1-(BETA-METHYLENE) PYROPHOSPHATE;1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribose;1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-D-ribose;1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-ribose' 
#
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
C1 C2 PPC sing 260 n n 
C1 O1 PPC sing 261 n n 
C1 O4 PPC sing 262 n n 
C1 H1 PPC sing 263 n n 
C2 C3 PPC sing 264 n n 
C2 O2 PPC sing 265 n n 
C2 H2 PPC sing 266 n n 
C3 C4 PPC sing 267 n n 
C3 O3 PPC sing 268 n n 
C3 H3 PPC sing 269 n n 
C4 C5 PPC sing 270 n n 
C4 O4 PPC sing 271 n n 
C4 H4 PPC sing 272 n n 
C5 O5 PPC sing 273 n n 
C5 H51 PPC sing 274 n n 
C5 H52 PPC sing 275 n n 
O1 PA PPC sing 276 n n 
O2 HO2 PPC sing 277 n n 
O3 HO3 PPC sing 278 n n 
P O1P PPC sing 279 n n 
P O2P PPC sing 280 n n 
P O3P PPC doub 281 n n 
P O5 PPC sing 282 n n 
O1P HO1P PPC sing 283 n n 
O2P HO2P PPC sing 284 n n 
PA O1A PPC sing 285 n n 
PA O2A PPC doub 286 n n 
PA C3A PPC sing 287 n n 
O1A HO1A PPC sing 288 n n 
PB O1B PPC sing 289 n n 
PB O2B PPC doub 290 n n 
PB O3B PPC sing 291 n n 
PB C3A PPC sing 292 n n 
O1B HO1B PPC sing 293 n n 
O3B HO3B PPC sing 294 n n 
C3A H3A1 PPC sing 295 n n 
C3A H3A2 PPC sing 296 n n 
#
_atom_sites.entry_id                     4WML 
_atom_sites.fract_transf_matrix[1][1]    0.016244 
_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]    0.016244 
_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]    0.007548 
_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 MG A 1 301 0 MG MG . 
C 3 PPC A 1 302 1 PPC PPC . 
D 4 HOH A 1 401 102 HOH HOH . 
D 4 HOH A 2 402 90 HOH HOH . 
D 4 HOH A 3 403 31 HOH HOH . 
D 4 HOH A 4 404 139 HOH HOH . 
D 4 HOH A 5 405 106 HOH HOH . 
D 4 HOH A 6 406 32 HOH HOH . 
D 4 HOH A 7 407 105 HOH HOH . 
D 4 HOH A 8 408 122 HOH HOH . 
D 4 HOH A 9 409 4 HOH HOH . 
D 4 HOH A 10 410 7 HOH HOH . 
D 4 HOH A 11 411 104 HOH HOH . 
D 4 HOH A 12 412 88 HOH HOH . 
D 4 HOH A 13 413 115 HOH HOH . 
D 4 HOH A 14 414 18 HOH HOH . 
D 4 HOH A 15 415 89 HOH HOH . 
D 4 HOH A 16 416 128 HOH HOH . 
D 4 HOH A 17 417 127 HOH HOH . 
D 4 HOH A 18 418 26 HOH HOH . 
D 4 HOH A 19 419 94 HOH HOH . 
D 4 HOH A 20 420 114 HOH HOH . 
D 4 HOH A 21 421 13 HOH HOH . 
D 4 HOH A 22 422 40 HOH HOH . 
D 4 HOH A 23 423 49 HOH HOH . 
D 4 HOH A 24 424 101 HOH HOH . 
D 4 HOH A 25 425 37 HOH HOH . 
D 4 HOH A 26 426 9 HOH HOH . 
D 4 HOH A 27 427 77 HOH HOH . 
D 4 HOH A 28 428 60 HOH HOH . 
D 4 HOH A 29 429 30 HOH HOH . 
D 4 HOH A 30 430 35 HOH HOH . 
D 4 HOH A 31 431 8 HOH HOH . 
D 4 HOH A 32 432 67 HOH HOH . 
D 4 HOH A 33 433 38 HOH HOH . 
D 4 HOH A 34 434 81 HOH HOH . 
D 4 HOH A 35 435 1 HOH HOH . 
D 4 HOH A 36 436 59 HOH HOH . 
D 4 HOH A 37 437 73 HOH HOH . 
D 4 HOH A 38 438 78 HOH HOH . 
D 4 HOH A 39 439 116 HOH HOH . 
D 4 HOH A 40 440 62 HOH HOH . 
D 4 HOH A 41 441 68 HOH HOH . 
D 4 HOH A 42 442 66 HOH HOH . 
D 4 HOH A 43 443 118 HOH HOH . 
D 4 HOH A 44 444 130 HOH HOH . 
D 4 HOH A 45 445 61 HOH HOH . 
D 4 HOH A 46 446 76 HOH HOH . 
D 4 HOH A 47 447 93 HOH HOH . 
D 4 HOH A 48 448 54 HOH HOH . 
D 4 HOH A 49 449 136 HOH HOH . 
D 4 HOH A 50 450 65 HOH HOH . 
D 4 HOH A 51 451 83 HOH HOH . 
D 4 HOH A 52 452 87 HOH HOH . 
D 4 HOH A 53 453 134 HOH HOH . 
D 4 HOH A 54 454 131 HOH HOH . 
D 4 HOH A 55 455 64 HOH HOH . 
D 4 HOH A 56 456 2 HOH HOH . 
D 4 HOH A 57 457 3 HOH HOH . 
D 4 HOH A 58 458 5 HOH HOH . 
D 4 HOH A 59 459 6 HOH HOH . 
D 4 HOH A 60 460 10 HOH HOH . 
D 4 HOH A 61 461 11 HOH HOH . 
D 4 HOH A 62 462 12 HOH HOH . 
D 4 HOH A 63 463 14 HOH HOH . 
D 4 HOH A 64 464 15 HOH HOH . 
D 4 HOH A 65 465 16 HOH HOH . 
D 4 HOH A 66 466 17 HOH HOH . 
D 4 HOH A 67 467 19 HOH HOH . 
D 4 HOH A 68 468 20 HOH HOH . 
D 4 HOH A 69 469 21 HOH HOH . 
D 4 HOH A 70 470 22 HOH HOH . 
D 4 HOH A 71 471 23 HOH HOH . 
D 4 HOH A 72 472 24 HOH HOH . 
D 4 HOH A 73 473 25 HOH HOH . 
D 4 HOH A 74 474 27 HOH HOH . 
D 4 HOH A 75 475 28 HOH HOH . 
D 4 HOH A 76 476 29 HOH HOH . 
D 4 HOH A 77 477 33 HOH HOH . 
D 4 HOH A 78 478 34 HOH HOH . 
D 4 HOH A 79 479 36 HOH HOH . 
D 4 HOH A 80 480 39 HOH HOH . 
D 4 HOH A 81 481 41 HOH HOH . 
D 4 HOH A 82 482 42 HOH HOH . 
D 4 HOH A 83 483 43 HOH HOH . 
D 4 HOH A 84 484 44 HOH HOH . 
D 4 HOH A 85 485 45 HOH HOH . 
D 4 HOH A 86 486 46 HOH HOH . 
D 4 HOH A 87 487 47 HOH HOH . 
D 4 HOH A 88 488 48 HOH HOH . 
D 4 HOH A 89 489 50 HOH HOH . 
D 4 HOH A 90 490 51 HOH HOH . 
D 4 HOH A 91 491 52 HOH HOH . 
D 4 HOH A 92 492 53 HOH HOH . 
D 4 HOH A 93 493 55 HOH HOH . 
D 4 HOH A 94 494 56 HOH HOH . 
D 4 HOH A 95 495 57 HOH HOH . 
D 4 HOH A 96 496 58 HOH HOH . 
D 4 HOH A 97 497 63 HOH HOH . 
D 4 HOH A 98 498 69 HOH HOH . 
D 4 HOH A 99 499 70 HOH HOH . 
D 4 HOH A 100 500 71 HOH HOH . 
D 4 HOH A 101 501 72 HOH HOH . 
D 4 HOH A 102 502 74 HOH HOH . 
D 4 HOH A 103 503 75 HOH HOH . 
D 4 HOH A 104 504 79 HOH HOH . 
D 4 HOH A 105 505 80 HOH HOH . 
D 4 HOH A 106 506 82 HOH HOH . 
D 4 HOH A 107 507 84 HOH HOH . 
D 4 HOH A 108 508 85 HOH HOH . 
D 4 HOH A 109 509 86 HOH HOH . 
D 4 HOH A 110 510 91 HOH HOH . 
D 4 HOH A 111 511 92 HOH HOH . 
D 4 HOH A 112 512 95 HOH HOH . 
D 4 HOH A 113 513 96 HOH HOH . 
D 4 HOH A 114 514 97 HOH HOH . 
D 4 HOH A 115 515 98 HOH HOH . 
D 4 HOH A 116 516 99 HOH HOH . 
D 4 HOH A 117 517 100 HOH HOH . 
D 4 HOH A 118 518 103 HOH HOH . 
D 4 HOH A 119 519 107 HOH HOH . 
D 4 HOH A 120 520 108 HOH HOH . 
D 4 HOH A 121 521 109 HOH HOH . 
D 4 HOH A 122 522 110 HOH HOH . 
D 4 HOH A 123 523 111 HOH HOH . 
D 4 HOH A 124 524 112 HOH HOH . 
D 4 HOH A 125 525 113 HOH HOH . 
D 4 HOH A 126 526 117 HOH HOH . 
D 4 HOH A 127 527 119 HOH HOH . 
D 4 HOH A 128 528 120 HOH HOH . 
D 4 HOH A 129 529 121 HOH HOH . 
D 4 HOH A 130 530 123 HOH HOH . 
D 4 HOH A 131 531 124 HOH HOH . 
D 4 HOH A 132 532 125 HOH HOH . 
D 4 HOH A 133 533 126 HOH HOH . 
D 4 HOH A 134 534 129 HOH HOH . 
D 4 HOH A 135 535 132 HOH HOH . 
D 4 HOH A 136 536 133 HOH HOH . 
D 4 HOH A 137 537 135 HOH HOH . 
D 4 HOH A 138 538 137 HOH HOH . 
D 4 HOH A 139 539 138 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 C C1 PPC . . . C 3 -4.909 -22.507 -2.875 1 30.91 ? C1 PPC 302 A 1 
HETATM 2 C C2 PPC . . . C 3 -4.077 -21.319 -3.332 1 30.89 ? C2 PPC 302 A 1 
HETATM 3 C C3 PPC . . . C 3 -4.264 -21.378 -4.848 1 30.75 ? C3 PPC 302 A 1 
HETATM 4 C C4 PPC . . . C 3 -4.783 -22.789 -5.159 1 33.72 ? C4 PPC 302 A 1 
HETATM 5 C C5 PPC . . . C 3 -3.893 -23.641 -6.006 1 37.65 ? C5 PPC 302 A 1 
HETATM 6 O O1 PPC . . . C 3 -6.26 -22.122 -2.792 1 29.44 ? O1 PPC 302 A 1 
HETATM 7 O O2 PPC . . . C 3 -4.638 -20.094 -2.729 1 27.98 ? O2 PPC 302 A 1 
HETATM 8 O O3 PPC . . . C 3 -5.337 -20.538 -5.212 1 29.89 ? O3 PPC 302 A 1 
HETATM 9 P P PPC . . . C 3 -3.849 -25.663 -7.368 1 32.85 ? P PPC 302 A 1 
HETATM 10 O O1P PPC . . . C 3 -3.011 -26.093 -6.187 1 42.71 ? O1P PPC 302 A 1 
HETATM 11 O O2P PPC . . . C 3 -4.739 -26.826 -7.8 1 44.02 ? O2P PPC 302 A 1 
HETATM 12 O O3P PPC . . . C 3 -2.967 -24.94 -8.412 1 35.46 ? O3P PPC 302 A 1 
HETATM 13 P PA PPC . . . C 3 -7.438 -23.111 -2.189 1 37.82 ? PA PPC 302 A 1 
HETATM 14 O O1A PPC . . . C 3 -6.708 -23.747 -1.087 1 36.32 ? O1A PPC 302 A 1 
HETATM 15 O O2A PPC . . . C 3 -8.078 -23.995 -3.372 1 38.71 ? O2A PPC 302 A 1 
HETATM 16 P PB PPC . . . C 3 -8.43 -20.551 -0.801 1 31.05 ? PB PPC 302 A 1 
HETATM 17 O O1B PPC . . . C 3 -9.772 -19.792 -0.556 1 23.57 ? O1B PPC 302 A 1 
HETATM 18 O O2B PPC . . . C 3 -7.424 -19.667 -1.764 1 32.27 ? O2B PPC 302 A 1 
HETATM 19 O O3B PPC . . . C 3 -7.702 -20.896 0.472 1 28.94 ? O3B PPC 302 A 1 
HETATM 20 C C3A PPC . . . C 3 -8.825 -22.092 -1.7 1 32.55 ? C3A PPC 302 A 1 
HETATM 21 O O5 PPC . . . C 3 -4.756 -24.555 -6.767 1 38.18 ? O5 PPC 302 A 1 
HETATM 22 O O4 PPC . . . C 3 -4.9 -23.467 -3.893 1 33.71 ? O4 PPC 302 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#