data_6B63 # _model_server_result.job_id TJz1AoSFl9MFM7GJVHXZHQ _model_server_result.datetime_utc '2024-11-14 19:03:52' _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 6b63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":509}' # _entry.id 6B63 # _exptl.entry_id 6B63 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.152 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '(2R)-2,3-dihydroxypropyl (2S)-2,3-dihydroxypropyl hydrogen phosphate' _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 90 _cell.angle_gamma 120 _cell.entry_id 6B63 _cell.length_a 89.645 _cell.length_b 89.645 _cell.length_c 101.915 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B63 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _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,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 C N N ? 2 J N N ? 2 K N N ? 2 L 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 OE1 GLU 67 A GLU 67 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc2 A OE2 GLU 67 A GLU 67 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc3 A OD1 ASP 82 A ASP 82 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc4 A OD2 ASP 82 A ASP 82 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc5 A OD2 ASP 82 A ASP 82 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc6 A O LEU 84 A LEU 84 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 A OD1 ASP 85 A ASP 85 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc8 A OD1 ASP 200 A ASP 200 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc9 D O4 PO4 . A PO4 502 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc10 D O2 PO4 . A PO4 502 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.717 ? metalc ? metalc11 D O1 PO4 . A PO4 502 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc12 D O2 PO4 . A PO4 502 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc13 E MG MG . A MG 503 1_555 S O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc14 E MG MG . A MG 503 1_555 S O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc15 F MG MG . A MG 504 1_555 S O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc16 B OE1 GLU 67 B GLU 67 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc17 B OE2 GLU 67 B GLU 67 1_555 R MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc18 B OD1 ASP 82 B ASP 82 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc19 B OD2 ASP 82 B ASP 82 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc20 B O LEU 84 B LEU 84 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc21 B OD1 ASP 85 B ASP 85 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc22 B OD1 ASP 200 B ASP 200 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc23 M O3 PO4 . B PO4 302 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc24 M O3 PO4 . B PO4 302 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc25 M O4 PO4 . B PO4 302 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.706 ? metalc ? metalc26 M O1 PO4 . B PO4 302 1_555 R MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc27 N MG MG . B MG 303 1_555 T O HOH . B HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? # _chem_comp.formula 'C6 H15 O8 P' _chem_comp.formula_weight 246.152 _chem_comp.id CU7 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2,3-dihydroxypropyl (2S)-2,3-dihydroxypropyl hydrogen phosphate' _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 O13 C12 CU7 sing 70 n n C12 C10 CU7 sing 71 n n C10 C9 CU7 sing 72 n n C10 O11 CU7 sing 73 n n C9 O8 CU7 sing 74 n n O8 P7 CU7 sing 75 n n O14 P7 CU7 doub 76 n n P7 O6 CU7 sing 77 n n P7 O15 CU7 sing 78 n n O4 C3 CU7 sing 79 n n O6 C5 CU7 sing 80 n n C5 C3 CU7 sing 81 n n C3 C2 CU7 sing 82 n n O1 C2 CU7 sing 83 n n C12 H1 CU7 sing 84 n n C12 H2 CU7 sing 85 n n O1 H3 CU7 sing 86 n n C2 H4 CU7 sing 87 n n C2 H5 CU7 sing 88 n n C3 H6 CU7 sing 89 n n C5 H7 CU7 sing 90 n n C5 H8 CU7 sing 91 n n O4 H9 CU7 sing 92 n n O15 H10 CU7 sing 93 n n C9 H11 CU7 sing 94 n n C9 H12 CU7 sing 95 n n C10 H13 CU7 sing 96 n n O13 H14 CU7 sing 97 n n O11 H15 CU7 sing 98 n n # _atom_sites.entry_id 6B63 _atom_sites.fract_transf_matrix[1][1] 0.011155 _atom_sites.fract_transf_matrix[1][2] 0.00644 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012881 _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] 0.009812 _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 CU7 A 1 501 501 CU7 GXX . D 3 PO4 A 1 502 901 PO4 PO4 . E 4 MG A 1 503 902 MG MG . F 4 MG A 1 504 903 MG MG . G 5 SO4 A 1 505 904 SO4 SO4 . H 6 EPE A 1 506 905 EPE EPE . I 4 MG A 1 507 906 MG MG . J 2 CU7 A 1 508 500 CU7 GXX . K 2 CU7 A 1 509 501 CU7 GXX . L 2 CU7 B 1 301 500 CU7 GXX . M 3 PO4 B 1 302 901 PO4 PO4 . N 4 MG B 1 303 902 MG MG . O 4 MG B 1 304 903 MG MG . P 5 SO4 B 1 305 904 SO4 SO4 . Q 6 EPE B 1 306 905 EPE EPE . R 4 MG B 1 307 906 MG MG . S 7 HOH A 1 601 3 HOH HOH . S 7 HOH A 2 602 78 HOH HOH . S 7 HOH A 3 603 2 HOH HOH . S 7 HOH A 4 604 56 HOH HOH . S 7 HOH A 5 605 22 HOH HOH . S 7 HOH A 6 606 60 HOH HOH . S 7 HOH A 7 607 93 HOH HOH . S 7 HOH A 8 609 54 HOH HOH . S 7 HOH A 9 610 1 HOH HOH . S 7 HOH A 10 611 99 HOH HOH . S 7 HOH A 11 612 12 HOH HOH . S 7 HOH A 12 613 41 HOH HOH . S 7 HOH A 13 614 29 HOH HOH . S 7 HOH A 14 615 24 HOH HOH . S 7 HOH A 15 616 87 HOH HOH . S 7 HOH A 16 617 98 HOH HOH . S 7 HOH A 17 618 73 HOH HOH . S 7 HOH A 18 619 32 HOH HOH . S 7 HOH A 19 620 42 HOH HOH . S 7 HOH A 20 621 79 HOH HOH . S 7 HOH A 21 622 50 HOH HOH . S 7 HOH A 22 623 49 HOH HOH . S 7 HOH A 23 624 77 HOH HOH . S 7 HOH A 24 625 13 HOH HOH . S 7 HOH A 25 626 95 HOH HOH . S 7 HOH A 26 627 51 HOH HOH . S 7 HOH A 27 628 61 HOH HOH . S 7 HOH A 28 629 89 HOH HOH . S 7 HOH A 29 630 52 HOH HOH . S 7 HOH A 30 631 109 HOH HOH . S 7 HOH A 31 632 106 HOH HOH . S 7 HOH A 32 633 68 HOH HOH . S 7 HOH A 33 634 25 HOH HOH . S 7 HOH A 34 635 75 HOH HOH . S 7 HOH A 35 636 36 HOH HOH . S 7 HOH A 36 637 59 HOH HOH . S 7 HOH A 37 638 62 HOH HOH . S 7 HOH A 38 639 48 HOH HOH . S 7 HOH A 39 640 105 HOH HOH . S 7 HOH A 40 641 76 HOH HOH . S 7 HOH A 41 642 96 HOH HOH . S 7 HOH A 42 643 85 HOH HOH . S 7 HOH A 43 644 39 HOH HOH . S 7 HOH A 44 645 47 HOH HOH . S 7 HOH A 45 646 107 HOH HOH . T 7 HOH B 1 401 88 HOH HOH . T 7 HOH B 2 402 81 HOH HOH . T 7 HOH B 3 403 91 HOH HOH . T 7 HOH B 4 404 86 HOH HOH . T 7 HOH B 5 406 37 HOH HOH . T 7 HOH B 6 407 69 HOH HOH . T 7 HOH B 7 408 11 HOH HOH . T 7 HOH B 8 409 16 HOH HOH . T 7 HOH B 9 410 30 HOH HOH . T 7 HOH B 10 411 44 HOH HOH . T 7 HOH B 11 412 70 HOH HOH . T 7 HOH B 12 413 34 HOH HOH . T 7 HOH B 13 414 27 HOH HOH . T 7 HOH B 14 415 6 HOH HOH . T 7 HOH B 15 416 57 HOH HOH . T 7 HOH B 16 417 35 HOH HOH . T 7 HOH B 17 418 46 HOH HOH . T 7 HOH B 18 419 58 HOH HOH . T 7 HOH B 19 420 97 HOH HOH . T 7 HOH B 20 421 33 HOH HOH . T 7 HOH B 21 422 45 HOH HOH . T 7 HOH B 22 423 94 HOH HOH . T 7 HOH B 23 424 71 HOH HOH . T 7 HOH B 24 425 63 HOH HOH . T 7 HOH B 25 426 40 HOH HOH . T 7 HOH B 26 427 102 HOH HOH . T 7 HOH B 27 428 66 HOH HOH . T 7 HOH B 28 429 74 HOH HOH . T 7 HOH B 29 430 104 HOH HOH . T 7 HOH B 30 431 55 HOH HOH . T 7 HOH B 31 432 84 HOH HOH . T 7 HOH B 32 433 65 HOH HOH . T 7 HOH B 33 434 64 HOH HOH . T 7 HOH B 34 435 101 HOH HOH . T 7 HOH B 35 436 103 HOH HOH . T 7 HOH B 36 437 100 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 C12 CU7 . . . K 2 -46.074 91.661 -12.631 1 75.36 ? C12 CU7 509 A 1 HETATM 2 O O1 CU7 . . . K 2 -48.769 96.066 -20.348 1 67.55 ? O1 CU7 509 A 1 HETATM 3 O O6 CU7 . . . K 2 -46.058 96.606 -16.459 1 81.88 ? O6 CU7 509 A 1 HETATM 4 C C2 CU7 . . . K 2 -47.842 95.886 -19.334 1 86.9 ? C2 CU7 509 A 1 HETATM 5 C C3 CU7 . . . K 2 -47.559 97.034 -18.406 1 101.35 ? C3 CU7 509 A 1 HETATM 6 C C5 CU7 . . . K 2 -47.338 96.587 -16.987 1 84.88 ? C5 CU7 509 A 1 HETATM 7 O O4 CU7 . . . K 2 -46.492 97.794 -18.847 1 60.23 ? O4 CU7 509 A 1 HETATM 8 O O15 CU7 . . . K 2 -43.92 95.62 -15.588 1 45.44 ? O15 CU7 509 A 1 HETATM 9 P P7 CU7 . . . K 2 -45.317 95.279 -16.068 1 101.41 ? P7 CU7 509 A 1 HETATM 10 O O14 CU7 . . . K 2 -45.164 94.398 -17.295 1 96.86 ? O14 CU7 509 A 1 HETATM 11 O O8 CU7 . . . K 2 -46.155 94.54 -14.959 1 67.42 ? O8 CU7 509 A 1 HETATM 12 C C9 CU7 . . . K 2 -45.609 93.621 -14.075 1 57.31 ? C9 CU7 509 A 1 HETATM 13 C C10 CU7 . . . K 2 -46.096 92.197 -14.04 1 78.44 ? C10 CU7 509 A 1 HETATM 14 O O13 CU7 . . . K 2 -46.329 90.323 -12.348 1 48.08 ? O13 CU7 509 A 1 HETATM 15 O O11 CU7 . . . K 2 -47.373 92.128 -14.562 1 77.68 ? O11 CU7 509 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #