data_6RA9 # _model_server_result.job_id nYsflXJdFDzdbcFPEfV57w _model_server_result.datetime_utc '2024-11-16 01:25:30' _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 6ra9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6RA9 # _exptl.entry_id 6RA9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 215.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE _entity.pdbx_number_of_molecules 3 _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 6RA9 _cell.length_a 133.52 _cell.length_b 133.52 _cell.length_c 305.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RA9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 ? 3 C N N ? 3 D N N ? 3 M 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 covale ? covale1 A C GLY 265 A GLY 265 1_555 A N POK 266 A POK 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C POK 266 A POK 266 1_555 A N VAL 267 A VAL 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C LEU 299 A LEU 299 1_555 A N SEP 300 A SEP 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C SEP 300 A SEP 300 1_555 A N GLU 301 A GLU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A CD GLU 301 A GLU 301 1_555 D N GPE . A GPE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale6 A CD GLU 374 A GLU 374 1_555 C N GPE . A GPE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale7 B C GLY 265 B GLY 265 1_555 B N POK 266 B POK 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 B C POK 266 B POK 266 1_555 B N VAL 267 B VAL 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 B CD GLU 374 B GLU 374 1_555 M N GPE . B GPE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? # _chem_comp.formula 'C5 H14 N O6 P' _chem_comp.formula_weight 215.142 _chem_comp.id GPE _chem_comp.mon_nstd_flag . _chem_comp.name L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE _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 P O11 GPE sing 187 n n P O12 GPE sing 188 n n P O14 GPE sing 189 n n P O13 GPE doub 190 n n O11 C1 GPE sing 191 n n O12 C11 GPE sing 192 n n O14 HO4 GPE sing 193 n n C1 C2 GPE sing 194 n n C1 H11 GPE sing 195 n n C1 H12 GPE sing 196 n n C2 C3 GPE sing 197 n n C2 O21 GPE sing 198 n n C2 H2 GPE sing 199 n n C3 O31 GPE sing 200 n n C3 H31 GPE sing 201 n n C3 H32 GPE sing 202 n n O31 HO1 GPE sing 203 n n O21 HO2 GPE sing 204 n n C11 C12 GPE sing 205 n n C11 H111 GPE sing 206 n n C11 H112 GPE sing 207 n n C12 N GPE sing 208 n n C12 H121 GPE sing 209 n n C12 H122 GPE sing 210 n n N HN1 GPE sing 211 n n N HN2 GPE sing 212 n n # _atom_sites.entry_id 6RA9 _atom_sites.fract_transf_matrix[1][1] 0.00749 _atom_sites.fract_transf_matrix[1][2] 0.004324 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008648 _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] 0.003274 _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 GPE A 1 501 374 GPE EF1 . D 3 GPE A 1 502 301 GPE EF1 . E 4 GDP A 1 503 501 GDP GDP . F 5 GOL A 1 504 502 GOL GOL . G 5 GOL A 1 505 503 GOL GOL . H 6 SO4 A 1 506 1 SO4 SO4 . I 6 SO4 A 1 507 2 SO4 SO4 . J 6 SO4 A 1 508 4 SO4 SO4 . K 6 SO4 A 1 509 9 SO4 SO4 . L 6 SO4 A 1 510 13 SO4 SO4 . M 3 GPE B 1 501 374 GPE EF1 . N 4 GDP B 1 502 501 GDP GDP . O 5 GOL B 1 503 502 GOL GOL . P 5 GOL B 1 504 503 GOL GOL . Q 5 GOL B 1 505 504 GOL GOL . R 5 GOL B 1 506 505 GOL GOL . S 6 SO4 B 1 507 5 SO4 SO4 . T 6 SO4 B 1 508 6 SO4 SO4 . U 6 SO4 B 1 509 8 SO4 SO4 . V 6 SO4 B 1 510 10 SO4 SO4 . W 6 SO4 B 1 511 11 SO4 SO4 . X 6 SO4 B 1 512 12 SO4 SO4 . Y 7 HOH A 1 601 87 HOH HOH . Y 7 HOH A 2 602 96 HOH HOH . Y 7 HOH A 3 603 24 HOH HOH . Y 7 HOH A 4 604 84 HOH HOH . Y 7 HOH A 5 605 4 HOH HOH . Y 7 HOH A 6 606 102 HOH HOH . Y 7 HOH A 7 607 82 HOH HOH . Y 7 HOH A 8 608 29 HOH HOH . Y 7 HOH A 9 609 104 HOH HOH . Y 7 HOH A 10 610 39 HOH HOH . Y 7 HOH A 11 611 16 HOH HOH . Y 7 HOH A 12 612 117 HOH HOH . Y 7 HOH A 13 613 50 HOH HOH . Y 7 HOH A 14 614 40 HOH HOH . Y 7 HOH A 15 615 110 HOH HOH . Y 7 HOH A 16 616 9 HOH HOH . Y 7 HOH A 17 617 33 HOH HOH . Y 7 HOH A 18 618 103 HOH HOH . Y 7 HOH A 19 619 13 HOH HOH . Y 7 HOH A 20 620 123 HOH HOH . Y 7 HOH A 21 621 83 HOH HOH . Y 7 HOH A 22 622 114 HOH HOH . Y 7 HOH A 23 623 21 HOH HOH . Y 7 HOH A 24 624 95 HOH HOH . Y 7 HOH A 25 625 18 HOH HOH . Y 7 HOH A 26 626 67 HOH HOH . Y 7 HOH A 27 627 99 HOH HOH . Y 7 HOH A 28 628 112 HOH HOH . Y 7 HOH A 29 629 25 HOH HOH . Y 7 HOH A 30 630 10 HOH HOH . Y 7 HOH A 31 631 46 HOH HOH . Y 7 HOH A 32 632 85 HOH HOH . Y 7 HOH A 33 633 5 HOH HOH . Y 7 HOH A 34 634 17 HOH HOH . Y 7 HOH A 35 635 120 HOH HOH . Y 7 HOH A 36 636 101 HOH HOH . Y 7 HOH A 37 637 56 HOH HOH . Y 7 HOH A 38 638 53 HOH HOH . Y 7 HOH A 39 639 119 HOH HOH . Y 7 HOH A 40 640 20 HOH HOH . Y 7 HOH A 41 641 1 HOH HOH . Y 7 HOH A 42 642 93 HOH HOH . Y 7 HOH A 43 643 6 HOH HOH . Y 7 HOH A 44 644 100 HOH HOH . Y 7 HOH A 45 645 54 HOH HOH . Y 7 HOH A 46 646 7 HOH HOH . Y 7 HOH A 47 647 12 HOH HOH . Y 7 HOH A 48 648 44 HOH HOH . Y 7 HOH A 49 649 45 HOH HOH . Y 7 HOH A 50 650 75 HOH HOH . Y 7 HOH A 51 651 125 HOH HOH . Y 7 HOH A 52 652 57 HOH HOH . Y 7 HOH A 53 653 78 HOH HOH . Y 7 HOH A 54 654 94 HOH HOH . Y 7 HOH A 55 655 121 HOH HOH . Y 7 HOH A 56 656 8 HOH HOH . Y 7 HOH A 57 657 98 HOH HOH . Y 7 HOH A 58 658 59 HOH HOH . Y 7 HOH A 59 659 73 HOH HOH . Y 7 HOH A 60 660 42 HOH HOH . Y 7 HOH A 61 661 14 HOH HOH . Y 7 HOH A 62 662 68 HOH HOH . Y 7 HOH A 63 663 47 HOH HOH . Z 7 HOH B 1 601 38 HOH HOH . Z 7 HOH B 2 602 122 HOH HOH . Z 7 HOH B 3 603 88 HOH HOH . Z 7 HOH B 4 604 34 HOH HOH . Z 7 HOH B 5 605 48 HOH HOH . Z 7 HOH B 6 606 31 HOH HOH . Z 7 HOH B 7 607 43 HOH HOH . Z 7 HOH B 8 608 91 HOH HOH . Z 7 HOH B 9 609 62 HOH HOH . Z 7 HOH B 10 610 89 HOH HOH . Z 7 HOH B 11 611 105 HOH HOH . Z 7 HOH B 12 612 116 HOH HOH . Z 7 HOH B 13 613 52 HOH HOH . Z 7 HOH B 14 614 70 HOH HOH . Z 7 HOH B 15 615 30 HOH HOH . Z 7 HOH B 16 616 11 HOH HOH . Z 7 HOH B 17 617 86 HOH HOH . Z 7 HOH B 18 618 51 HOH HOH . Z 7 HOH B 19 619 113 HOH HOH . Z 7 HOH B 20 620 26 HOH HOH . Z 7 HOH B 21 621 97 HOH HOH . Z 7 HOH B 22 622 22 HOH HOH . Z 7 HOH B 23 623 74 HOH HOH . Z 7 HOH B 24 624 79 HOH HOH . Z 7 HOH B 25 625 81 HOH HOH . Z 7 HOH B 26 626 15 HOH HOH . Z 7 HOH B 27 627 72 HOH HOH . Z 7 HOH B 28 628 77 HOH HOH . Z 7 HOH B 29 629 3 HOH HOH . Z 7 HOH B 30 630 19 HOH HOH . Z 7 HOH B 31 631 118 HOH HOH . Z 7 HOH B 32 632 106 HOH HOH . Z 7 HOH B 33 633 108 HOH HOH . Z 7 HOH B 34 634 27 HOH HOH . Z 7 HOH B 35 635 76 HOH HOH . Z 7 HOH B 36 636 63 HOH HOH . Z 7 HOH B 37 637 111 HOH HOH . Z 7 HOH B 38 638 49 HOH HOH . Z 7 HOH B 39 639 28 HOH HOH . Z 7 HOH B 40 640 37 HOH HOH . Z 7 HOH B 41 641 90 HOH HOH . Z 7 HOH B 42 642 124 HOH HOH . Z 7 HOH B 43 643 58 HOH HOH . Z 7 HOH B 44 644 61 HOH HOH . Z 7 HOH B 45 645 23 HOH HOH . Z 7 HOH B 46 646 115 HOH HOH . Z 7 HOH B 47 647 80 HOH HOH . Z 7 HOH B 48 648 107 HOH HOH . Z 7 HOH B 49 649 60 HOH HOH . Z 7 HOH B 50 650 64 HOH HOH . Z 7 HOH B 51 651 66 HOH HOH . Z 7 HOH B 52 652 35 HOH HOH . Z 7 HOH B 53 653 41 HOH HOH . Z 7 HOH B 54 654 71 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 P P GPE . . . D 3 47.21 6.378 2.058 0.8 161.17 ? P GPE 502 A 1 HETATM 2 O O11 GPE . . . D 3 48.827 6.227 1.741 0.8 153.61 ? O11 GPE 502 A 1 HETATM 3 O O12 GPE . . . D 3 46.88 7.823 2.819 0.8 146.99 ? O12 GPE 502 A 1 HETATM 4 O O14 GPE . . . D 3 46.717 5.241 2.846 0.8 168.78 -1 O14 GPE 502 A 1 HETATM 5 O O13 GPE . . . D 3 46.416 6.232 0.832 0.8 164.65 ? O13 GPE 502 A 1 HETATM 6 C C1 GPE . . . D 3 49.469 5.048 2.164 0.8 149.47 ? C1 GPE 502 A 1 HETATM 7 C C2 GPE . . . D 3 50.677 4.734 1.256 0.8 137.77 ? C2 GPE 502 A 1 HETATM 8 C C3 GPE . . . D 3 50.747 3.229 1.018 0.8 138.24 ? C3 GPE 502 A 1 HETATM 9 O O31 GPE . . . D 3 51.843 2.931 0.167 0.8 129.91 ? O31 GPE 502 A 1 HETATM 10 O O21 GPE . . . D 3 50.541 5.391 0.036 0.8 126.05 ? O21 GPE 502 A 1 HETATM 11 C C11 GPE . . . D 3 47.009 7.891 4.204 0.8 134.28 ? C11 GPE 502 A 1 HETATM 12 C C12 GPE . . . D 3 48.516 7.681 4.591 0.8 119.73 ? C12 GPE 502 A 1 HETATM 13 N N GPE . . . D 3 49.08 8.973 4.981 1 106.36 ? N GPE 502 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 13 #