data_2PMD
#
_model_server_result.job_id            rn_O7pIcrwWCthf87HRIMA 
_model_server_result.datetime_utc      '2024-11-17 14:23:46' 
_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          2pmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":420}' 
#
_entry.id    2PMD 
#
_exptl.entry_id    2PMD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              177.975 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            PYROPHOSPHATE 
_entity.pdbx_number_of_molecules    6 
_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            2PMD 
_cell.length_a            95.06 
_cell.length_b            95.06 
_cell.length_c            165.67 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PMD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,L 1 1 
B,H,I,J,K,M 2 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 E N N 
? 4 F N N 
? 4 G N N 
? 4 I N N 
? 4 J N N 
? 4 K 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
disulf ? disulf1 A SG CYS 59 A CYS 59 1_555 A SG CYS 74 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 62 A CYS 62 1_555 A SG CYS 77 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 B SG CYS 59 B CYS 59 1_555 B SG CYS 74 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf4 B SG CYS 62 B CYS 62 1_555 B SG CYS 77 B CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_chem_comp.formula           'H4 O7 P2' 
_chem_comp.formula_weight    177.975 
_chem_comp.id                PPV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              PYROPHOSPHATE 
_chem_comp.type              non-polymer 
_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
O11 P1 PPV sing 356 n n 
O11 H11 PPV sing 357 n n 
P1 O21 PPV sing 358 n n 
P1 O31 PPV doub 359 n n 
P1 OPP PPV sing 360 n n 
O21 H21 PPV sing 361 n n 
OPP P2 PPV sing 362 n n 
P2 O12 PPV sing 363 n n 
P2 O22 PPV doub 364 n n 
P2 O32 PPV sing 365 n n 
O12 H12 PPV sing 366 n n 
O32 H32 PPV sing 367 n n 
#
_atom_sites.entry_id                     2PMD 
_atom_sites.fract_transf_matrix[1][1]    0.01052 
_atom_sites.fract_transf_matrix[1][2]    0.006074 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012147 
_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]    0.006036 
_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 GDP A 1 416 201 GDP GDP . 
D 3 GNP A 1 417 203 GNP GNP . 
E 4 PPV A 1 418 205 PPV PPV . 
F 4 PPV A 1 419 206 PPV PPV . 
G 4 PPV A 1 420 209 PPV PPV . 
H 2 GDP B 1 416 202 GDP GDP . 
I 4 PPV B 1 417 204 PPV PPV . 
J 4 PPV B 1 418 207 PPV PPV . 
K 4 PPV B 1 419 208 PPV PPV . 
L 5 HOH A 1 421 0 HOH HOH . 
L 5 HOH A 2 422 1 HOH HOH . 
L 5 HOH A 3 423 4 HOH HOH . 
L 5 HOH A 4 424 6 HOH HOH . 
L 5 HOH A 5 425 8 HOH HOH . 
L 5 HOH A 6 426 9 HOH HOH . 
L 5 HOH A 7 427 10 HOH HOH . 
L 5 HOH A 8 428 12 HOH HOH . 
L 5 HOH A 9 429 17 HOH HOH . 
L 5 HOH A 10 430 20 HOH HOH . 
L 5 HOH A 11 431 24 HOH HOH . 
L 5 HOH A 12 432 29 HOH HOH . 
L 5 HOH A 13 433 30 HOH HOH . 
L 5 HOH A 14 434 37 HOH HOH . 
L 5 HOH A 15 435 39 HOH HOH . 
L 5 HOH A 16 436 42 HOH HOH . 
L 5 HOH A 17 437 43 HOH HOH . 
L 5 HOH A 18 438 47 HOH HOH . 
L 5 HOH A 19 439 51 HOH HOH . 
L 5 HOH A 20 440 53 HOH HOH . 
L 5 HOH A 21 441 54 HOH HOH . 
L 5 HOH A 22 442 58 HOH HOH . 
L 5 HOH A 23 443 59 HOH HOH . 
L 5 HOH A 24 444 60 HOH HOH . 
L 5 HOH A 25 445 61 HOH HOH . 
L 5 HOH A 26 446 62 HOH HOH . 
L 5 HOH A 27 447 65 HOH HOH . 
L 5 HOH A 28 448 66 HOH HOH . 
L 5 HOH A 29 449 67 HOH HOH . 
L 5 HOH A 30 450 69 HOH HOH . 
L 5 HOH A 31 451 73 HOH HOH . 
L 5 HOH A 32 452 74 HOH HOH . 
L 5 HOH A 33 453 77 HOH HOH . 
L 5 HOH A 34 454 80 HOH HOH . 
L 5 HOH A 35 455 81 HOH HOH . 
L 5 HOH A 36 456 83 HOH HOH . 
L 5 HOH A 37 457 85 HOH HOH . 
L 5 HOH A 38 458 89 HOH HOH . 
L 5 HOH A 39 459 90 HOH HOH . 
L 5 HOH A 40 460 91 HOH HOH . 
L 5 HOH A 41 461 99 HOH HOH . 
L 5 HOH A 42 462 101 HOH HOH . 
L 5 HOH A 43 463 102 HOH HOH . 
L 5 HOH A 44 464 103 HOH HOH . 
L 5 HOH A 45 465 109 HOH HOH . 
L 5 HOH A 46 466 116 HOH HOH . 
L 5 HOH A 47 467 117 HOH HOH . 
L 5 HOH A 48 468 119 HOH HOH . 
L 5 HOH A 49 469 120 HOH HOH . 
L 5 HOH A 50 470 123 HOH HOH . 
L 5 HOH A 51 471 125 HOH HOH . 
L 5 HOH A 52 472 128 HOH HOH . 
L 5 HOH A 53 473 129 HOH HOH . 
L 5 HOH A 54 474 130 HOH HOH . 
L 5 HOH A 55 475 132 HOH HOH . 
L 5 HOH A 56 476 134 HOH HOH . 
L 5 HOH A 57 477 137 HOH HOH . 
L 5 HOH A 58 478 139 HOH HOH . 
L 5 HOH A 59 479 143 HOH HOH . 
L 5 HOH A 60 480 145 HOH HOH . 
L 5 HOH A 61 481 148 HOH HOH . 
L 5 HOH A 62 482 150 HOH HOH . 
L 5 HOH A 63 483 151 HOH HOH . 
L 5 HOH A 64 484 154 HOH HOH . 
L 5 HOH A 65 485 156 HOH HOH . 
L 5 HOH A 66 486 157 HOH HOH . 
L 5 HOH A 67 487 160 HOH HOH . 
L 5 HOH A 68 488 164 HOH HOH . 
L 5 HOH A 69 489 166 HOH HOH . 
L 5 HOH A 70 490 170 HOH HOH . 
L 5 HOH A 71 491 172 HOH HOH . 
M 5 HOH B 1 420 2 HOH HOH . 
M 5 HOH B 2 421 3 HOH HOH . 
M 5 HOH B 3 422 5 HOH HOH . 
M 5 HOH B 4 423 7 HOH HOH . 
M 5 HOH B 5 424 11 HOH HOH . 
M 5 HOH B 6 425 14 HOH HOH . 
M 5 HOH B 7 426 15 HOH HOH . 
M 5 HOH B 8 427 16 HOH HOH . 
M 5 HOH B 9 428 18 HOH HOH . 
M 5 HOH B 10 429 19 HOH HOH . 
M 5 HOH B 11 430 21 HOH HOH . 
M 5 HOH B 12 431 22 HOH HOH . 
M 5 HOH B 13 432 23 HOH HOH . 
M 5 HOH B 14 433 25 HOH HOH . 
M 5 HOH B 15 434 26 HOH HOH . 
M 5 HOH B 16 435 27 HOH HOH . 
M 5 HOH B 17 436 28 HOH HOH . 
M 5 HOH B 18 437 31 HOH HOH . 
M 5 HOH B 19 438 32 HOH HOH . 
M 5 HOH B 20 439 33 HOH HOH . 
M 5 HOH B 21 440 34 HOH HOH . 
M 5 HOH B 22 441 35 HOH HOH . 
M 5 HOH B 23 442 36 HOH HOH . 
M 5 HOH B 24 443 38 HOH HOH . 
M 5 HOH B 25 444 40 HOH HOH . 
M 5 HOH B 26 445 41 HOH HOH . 
M 5 HOH B 27 446 44 HOH HOH . 
M 5 HOH B 28 447 45 HOH HOH . 
M 5 HOH B 29 448 46 HOH HOH . 
M 5 HOH B 30 449 48 HOH HOH . 
M 5 HOH B 31 450 49 HOH HOH . 
M 5 HOH B 32 451 50 HOH HOH . 
M 5 HOH B 33 452 52 HOH HOH . 
M 5 HOH B 34 453 55 HOH HOH . 
M 5 HOH B 35 454 56 HOH HOH . 
M 5 HOH B 36 455 57 HOH HOH . 
M 5 HOH B 37 456 68 HOH HOH . 
M 5 HOH B 38 457 70 HOH HOH . 
M 5 HOH B 39 458 71 HOH HOH . 
M 5 HOH B 40 459 75 HOH HOH . 
M 5 HOH B 41 460 78 HOH HOH . 
M 5 HOH B 42 461 82 HOH HOH . 
M 5 HOH B 43 462 84 HOH HOH . 
M 5 HOH B 44 463 87 HOH HOH . 
M 5 HOH B 45 464 88 HOH HOH . 
M 5 HOH B 46 465 92 HOH HOH . 
M 5 HOH B 47 466 93 HOH HOH . 
M 5 HOH B 48 467 94 HOH HOH . 
M 5 HOH B 49 468 95 HOH HOH . 
M 5 HOH B 50 469 96 HOH HOH . 
M 5 HOH B 51 470 97 HOH HOH . 
M 5 HOH B 52 471 98 HOH HOH . 
M 5 HOH B 53 472 100 HOH HOH . 
M 5 HOH B 54 473 104 HOH HOH . 
M 5 HOH B 55 474 105 HOH HOH . 
M 5 HOH B 56 475 106 HOH HOH . 
M 5 HOH B 57 476 107 HOH HOH . 
M 5 HOH B 58 477 112 HOH HOH . 
M 5 HOH B 59 478 113 HOH HOH . 
M 5 HOH B 60 479 114 HOH HOH . 
M 5 HOH B 61 480 115 HOH HOH . 
M 5 HOH B 62 481 118 HOH HOH . 
M 5 HOH B 63 482 121 HOH HOH . 
M 5 HOH B 64 483 122 HOH HOH . 
M 5 HOH B 65 484 126 HOH HOH . 
M 5 HOH B 66 485 127 HOH HOH . 
M 5 HOH B 67 486 131 HOH HOH . 
M 5 HOH B 68 487 135 HOH HOH . 
M 5 HOH B 69 488 138 HOH HOH . 
M 5 HOH B 70 489 140 HOH HOH . 
M 5 HOH B 71 490 141 HOH HOH . 
M 5 HOH B 72 491 142 HOH HOH . 
M 5 HOH B 73 492 144 HOH HOH . 
M 5 HOH B 74 493 147 HOH HOH . 
M 5 HOH B 75 494 149 HOH HOH . 
M 5 HOH B 76 495 152 HOH HOH . 
M 5 HOH B 77 496 153 HOH HOH . 
M 5 HOH B 78 497 155 HOH HOH . 
M 5 HOH B 79 498 158 HOH HOH . 
M 5 HOH B 80 499 159 HOH HOH . 
M 5 HOH B 81 500 161 HOH HOH . 
M 5 HOH B 82 501 162 HOH HOH . 
M 5 HOH B 83 502 163 HOH HOH . 
M 5 HOH B 84 503 165 HOH HOH . 
M 5 HOH B 85 504 167 HOH HOH . 
M 5 HOH B 86 505 168 HOH HOH . 
M 5 HOH B 87 506 169 HOH HOH . 
M 5 HOH B 88 507 171 HOH HOH . 
M 5 HOH B 89 508 173 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 O O11 PPV . . . G 4 26.892 14.679 12.811 1 167.34 ? O11 PPV 420 A 1 
HETATM 2 P P1 PPV . . . G 4 28.282 14.894 13.269 0.97 167.29 ? P1 PPV 420 A 1 
HETATM 3 O O21 PPV . . . G 4 28.303 16.129 14.311 1 167.24 ? O21 PPV 420 A 1 
HETATM 4 O O31 PPV . . . G 4 29.224 15.237 12.01 1 166.85 ? O31 PPV 420 A 1 
HETATM 5 O OPP PPV . . . G 4 28.837 13.55 14.014 1 167.93 ? OPP PPV 420 A 1 
HETATM 6 P P2 PPV . . . G 4 28.827 12.277 12.99 0.98 168.08 ? P2 PPV 420 A 1 
HETATM 7 O O12 PPV . . . G 4 27.446 12.013 12.525 1 168.37 ? O12 PPV 420 A 1 
HETATM 8 O O22 PPV . . . G 4 29.772 12.581 11.727 0.98 167.89 ? O22 PPV 420 A 1 
HETATM 9 O O32 PPV . . . G 4 29.378 10.964 13.746 0.93 167.89 ? O32 PPV 420 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    54 
_model_server_stats.query_time_ms           361 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           9 
#