data_6W2L
#
_model_server_result.job_id            a_xjBEBi997K0gFRj-Qb_Q 
_model_server_result.datetime_utc      '2024-11-26 06:59:00' 
_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          6w2l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    6W2L 
#
_exptl.entry_id    6W2L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              246.092 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' 
_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         120 
_cell.entry_id            6W2L 
_cell.length_a            185.67 
_cell.length_b            185.67 
_cell.length_c            113.351 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6W2L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_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,G 
_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
? 4 D N N 
? 4 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
metalc ? metalc1 A OD1 ASP 34 A ASP 34 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? 
metalc ? metalc2 C MG MG . A MG 401 1_555 D O2A IPE . A IPE 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc3 C MG MG . A MG 401 1_555 D O3B IPE . A IPE 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc4 C MG MG . A MG 401 1_555 E O1A IPE . A IPE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc5 C MG MG . A MG 401 1_555 F O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
#
_chem_comp.formula           'C5 H12 O7 P2' 
_chem_comp.formula_weight    246.092 
_chem_comp.id                IPE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ISOPENTENYL PYROPHOSPHATE' 
#
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 O1 IPE sing 173 n n 
C1 C2 IPE sing 174 n n 
C1 H11 IPE sing 175 n n 
C1 H12 IPE sing 176 n n 
O1 PA IPE sing 177 n n 
C2 C3 IPE sing 178 n n 
C2 H21 IPE sing 179 n n 
C2 H22 IPE sing 180 n n 
C3 C4 IPE doub 181 n n 
C3 C5 IPE sing 182 n n 
C4 H41 IPE sing 183 n n 
C4 H42 IPE sing 184 n n 
C5 H51 IPE sing 185 n n 
C5 H52 IPE sing 186 n n 
C5 H53 IPE sing 187 n n 
PA O1A IPE doub 188 n n 
PA O2A IPE sing 189 n n 
PA O3A IPE sing 190 n n 
O2A H2A IPE sing 191 n n 
O3A PB IPE sing 192 n n 
PB O1B IPE sing 193 n n 
PB O2B IPE doub 194 n n 
PB O3B IPE sing 195 n n 
O1B H1B IPE sing 196 n n 
O3B H3B IPE sing 197 n n 
#
_atom_sites.entry_id                     6W2L 
_atom_sites.fract_transf_matrix[1][1]    0.005386 
_atom_sites.fract_transf_matrix[1][2]    0.00311 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006219 
_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]    0.008822 
_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 3 MG A 1 401 1 MG MG . 
D 4 IPE A 1 402 2 IPE DRG . 
E 4 IPE A 1 403 3 IPE DRG . 
F 5 HOH A 1 501 83 HOH HOH . 
F 5 HOH A 2 502 5 HOH HOH . 
F 5 HOH A 3 503 154 HOH HOH . 
F 5 HOH A 4 504 106 HOH HOH . 
F 5 HOH A 5 505 27 HOH HOH . 
F 5 HOH A 6 506 401 HOH HOH . 
F 5 HOH A 7 507 121 HOH HOH . 
F 5 HOH A 8 508 132 HOH HOH . 
F 5 HOH A 9 509 50 HOH HOH . 
F 5 HOH A 10 510 74 HOH HOH . 
F 5 HOH A 11 511 88 HOH HOH . 
F 5 HOH A 12 512 128 HOH HOH . 
F 5 HOH A 13 513 77 HOH HOH . 
F 5 HOH A 14 514 75 HOH HOH . 
F 5 HOH A 15 515 103 HOH HOH . 
F 5 HOH A 16 516 109 HOH HOH . 
F 5 HOH A 17 517 107 HOH HOH . 
F 5 HOH A 18 518 38 HOH HOH . 
F 5 HOH A 19 519 117 HOH HOH . 
F 5 HOH A 20 520 123 HOH HOH . 
F 5 HOH A 21 521 125 HOH HOH . 
F 5 HOH A 22 522 134 HOH HOH . 
F 5 HOH A 23 523 126 HOH HOH . 
F 5 HOH A 24 524 153 HOH HOH . 
F 5 HOH A 25 525 110 HOH HOH . 
F 5 HOH A 26 526 54 HOH HOH . 
F 5 HOH A 27 527 7 HOH HOH . 
F 5 HOH A 28 528 122 HOH HOH . 
F 5 HOH A 29 529 155 HOH HOH . 
F 5 HOH A 30 530 13 HOH HOH . 
F 5 HOH A 31 531 53 HOH HOH . 
F 5 HOH A 32 532 102 HOH HOH . 
F 5 HOH A 33 533 91 HOH HOH . 
F 5 HOH A 34 534 118 HOH HOH . 
F 5 HOH A 35 535 104 HOH HOH . 
F 5 HOH A 36 536 78 HOH HOH . 
F 5 HOH A 37 537 3 HOH HOH . 
F 5 HOH A 38 538 80 HOH HOH . 
F 5 HOH A 39 539 45 HOH HOH . 
F 5 HOH A 40 540 43 HOH HOH . 
F 5 HOH A 41 541 116 HOH HOH . 
F 5 HOH A 42 542 87 HOH HOH . 
F 5 HOH A 43 543 115 HOH HOH . 
F 5 HOH A 44 544 12 HOH HOH . 
F 5 HOH A 45 545 11 HOH HOH . 
F 5 HOH A 46 546 90 HOH HOH . 
F 5 HOH A 47 547 46 HOH HOH . 
F 5 HOH A 48 548 119 HOH HOH . 
F 5 HOH A 49 549 108 HOH HOH . 
F 5 HOH A 50 550 120 HOH HOH . 
F 5 HOH A 51 551 41 HOH HOH . 
F 5 HOH A 52 552 47 HOH HOH . 
F 5 HOH A 53 553 22 HOH HOH . 
F 5 HOH A 54 554 79 HOH HOH . 
F 5 HOH A 55 555 137 HOH HOH . 
F 5 HOH A 56 556 92 HOH HOH . 
F 5 HOH A 57 557 114 HOH HOH . 
F 5 HOH A 58 558 42 HOH HOH . 
F 5 HOH A 59 559 111 HOH HOH . 
F 5 HOH A 60 560 133 HOH HOH . 
F 5 HOH A 61 561 24 HOH HOH . 
F 5 HOH A 62 562 105 HOH HOH . 
F 5 HOH A 63 563 113 HOH HOH . 
F 5 HOH A 64 564 85 HOH HOH . 
F 5 HOH A 65 565 93 HOH HOH . 
F 5 HOH A 66 566 112 HOH HOH . 
F 5 HOH A 67 567 49 HOH HOH . 
F 5 HOH A 68 568 76 HOH HOH . 
G 5 HOH B 1 301 96 HOH HOH . 
G 5 HOH B 2 302 2 HOH HOH . 
G 5 HOH B 3 303 58 HOH HOH . 
G 5 HOH B 4 304 101 HOH HOH . 
G 5 HOH B 5 305 68 HOH HOH . 
G 5 HOH B 6 306 34 HOH HOH . 
G 5 HOH B 7 307 19 HOH HOH . 
G 5 HOH B 8 308 156 HOH HOH . 
G 5 HOH B 9 309 142 HOH HOH . 
G 5 HOH B 10 310 70 HOH HOH . 
G 5 HOH B 11 311 56 HOH HOH . 
G 5 HOH B 12 312 17 HOH HOH . 
G 5 HOH B 13 313 131 HOH HOH . 
G 5 HOH B 14 314 151 HOH HOH . 
G 5 HOH B 15 315 157 HOH HOH . 
G 5 HOH B 16 316 94 HOH HOH . 
G 5 HOH B 17 317 144 HOH HOH . 
G 5 HOH B 18 318 158 HOH HOH . 
G 5 HOH B 19 319 141 HOH HOH . 
G 5 HOH B 20 320 61 HOH HOH . 
G 5 HOH B 21 321 65 HOH HOH . 
G 5 HOH B 22 322 146 HOH HOH . 
G 5 HOH B 23 323 6 HOH HOH . 
G 5 HOH B 24 324 10 HOH HOH . 
G 5 HOH B 25 325 73 HOH HOH . 
G 5 HOH B 26 326 150 HOH HOH . 
G 5 HOH B 27 327 140 HOH HOH . 
G 5 HOH B 28 328 9 HOH HOH . 
G 5 HOH B 29 329 152 HOH HOH . 
G 5 HOH B 30 330 143 HOH HOH . 
G 5 HOH B 31 331 32 HOH HOH . 
G 5 HOH B 32 332 33 HOH HOH . 
G 5 HOH B 33 333 148 HOH HOH . 
G 5 HOH B 34 334 145 HOH HOH . 
G 5 HOH B 35 335 62 HOH HOH . 
G 5 HOH B 36 336 57 HOH HOH . 
G 5 HOH B 37 337 149 HOH HOH . 
G 5 HOH B 38 338 138 HOH HOH . 
G 5 HOH B 39 339 67 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 IPE . . . D 4 -5.139 -30.134 -48.457 1 64.96 ? C1 IPE 402 A 1 
HETATM 2 O O1 IPE . . . D 4 -5.506 -29.72 -49.782 1 63.35 ? O1 IPE 402 A 1 
HETATM 3 C C2 IPE . . . D 4 -4 -31.156 -48.506 1 72.23 ? C2 IPE 402 A 1 
HETATM 4 C C3 IPE . . . D 4 -4.393 -32.628 -48.265 1 74.34 ? C3 IPE 402 A 1 
HETATM 5 C C4 IPE . . . D 4 -3.3 -33.688 -48.337 1 75.9 ? C4 IPE 402 A 1 
HETATM 6 C C5 IPE . . . D 4 -5.848 -33.045 -47.95 1 65.53 ? C5 IPE 402 A 1 
HETATM 7 P PA IPE . . . D 4 -6.407 -30.646 -50.74 1 62.17 ? PA IPE 402 A 1 
HETATM 8 O O1A IPE . . . D 4 -5.67 -31.81 -51.302 1 68.68 ? O1A IPE 402 A 1 
HETATM 9 O O2A IPE . . . D 4 -7.688 -31.079 -49.829 1 65.11 ? O2A IPE 402 A 1 
HETATM 10 O O3A IPE . . . D 4 -6.941 -29.705 -51.932 1 65.6 ? O3A IPE 402 A 1 
HETATM 11 P PB IPE . . . D 4 -8.462 -29.131 -51.917 1 65.49 ? PB IPE 402 A 1 
HETATM 12 O O1B IPE . . . D 4 -9.358 -30.226 -52.731 1 64.47 ? O1B IPE 402 A 1 
HETATM 13 O O2B IPE . . . D 4 -8.431 -27.79 -52.845 1 62.23 ? O2B IPE 402 A 1 
HETATM 14 O O3B IPE . . . D 4 -9.002 -28.869 -50.551 1 59.46 ? O3B IPE 402 A 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           14 
#