data_6JCJ # _model_server_result.job_id y8y96DxVGq32G-oJy54uzw _model_server_result.datetime_utc '2025-02-17 10:27:49' _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 6jcj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 6JCJ # _exptl.entry_id 6JCJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 6JCJ _cell.length_a 105.544 _cell.length_b 157.329 _cell.length_c 184.031 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JCJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 _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 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id R _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 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc10 H MG MG . A MG 502 1_555 S O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc11 H MG MG . A MG 502 1_555 S O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc12 H MG MG . A MG 502 1_555 S O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc13 H MG MG . A MG 502 1_555 S O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc15 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc16 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc17 C OD1 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc18 C OD2 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc19 C O THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc20 C OG1 THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc21 C O GLY 44 C GLY 44 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc22 C OE1 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc23 C OE2 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc24 M O1G GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc25 M O1B GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc26 N MG MG . C MG 502 1_555 U O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc27 N MG MG . C MG 502 1_555 U O HOH . C HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc28 N MG MG . C MG 502 1_555 U O HOH . C HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc29 N MG MG . C MG 502 1_555 U O HOH . C HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 6JCJ _atom_sites.fract_transf_matrix[1][1] 0.009475 _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] 0.006356 _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] 0.005434 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 BG0 B 1 503 1 BG0 CRO . M 5 GTP C 1 501 501 GTP GTP . N 6 MG C 1 502 502 MG MG . O 7 CA C 1 503 1 CA CA . P 5 GTP D 1 501 501 GTP GTP . Q 9 BG0 D 1 502 2 BG0 CRO . R 10 ACP F 1 401 401 ACP ACP . S 11 HOH A 1 601 24 HOH HOH . S 11 HOH A 2 602 70 HOH HOH . S 11 HOH A 3 603 74 HOH HOH . S 11 HOH A 4 604 39 HOH HOH . S 11 HOH A 5 605 32 HOH HOH . S 11 HOH A 6 606 52 HOH HOH . S 11 HOH A 7 607 73 HOH HOH . S 11 HOH A 8 608 46 HOH HOH . S 11 HOH A 9 609 33 HOH HOH . S 11 HOH A 10 610 72 HOH HOH . S 11 HOH A 11 611 71 HOH HOH . S 11 HOH A 12 612 23 HOH HOH . S 11 HOH A 13 613 29 HOH HOH . S 11 HOH A 14 614 57 HOH HOH . S 11 HOH A 15 615 45 HOH HOH . S 11 HOH A 16 616 63 HOH HOH . T 11 HOH B 1 601 85 HOH HOH . T 11 HOH B 2 602 58 HOH HOH . T 11 HOH B 3 603 67 HOH HOH . T 11 HOH B 4 604 41 HOH HOH . T 11 HOH B 5 605 55 HOH HOH . T 11 HOH B 6 606 26 HOH HOH . T 11 HOH B 7 607 60 HOH HOH . T 11 HOH B 8 608 16 HOH HOH . T 11 HOH B 9 609 1 HOH HOH . T 11 HOH B 10 610 36 HOH HOH . T 11 HOH B 11 611 2 HOH HOH . T 11 HOH B 12 612 25 HOH HOH . T 11 HOH B 13 613 86 HOH HOH . T 11 HOH B 14 614 80 HOH HOH . T 11 HOH B 15 615 10 HOH HOH . T 11 HOH B 16 616 78 HOH HOH . U 11 HOH C 1 601 37 HOH HOH . U 11 HOH C 2 602 15 HOH HOH . U 11 HOH C 3 603 48 HOH HOH . U 11 HOH C 4 604 40 HOH HOH . U 11 HOH C 5 605 22 HOH HOH . U 11 HOH C 6 606 44 HOH HOH . U 11 HOH C 7 607 49 HOH HOH . U 11 HOH C 8 608 35 HOH HOH . U 11 HOH C 9 609 30 HOH HOH . U 11 HOH C 10 610 50 HOH HOH . U 11 HOH C 11 611 9 HOH HOH . U 11 HOH C 12 612 59 HOH HOH . U 11 HOH C 13 613 4 HOH HOH . U 11 HOH C 14 614 11 HOH HOH . U 11 HOH C 15 615 6 HOH HOH . U 11 HOH C 16 616 77 HOH HOH . U 11 HOH C 17 617 76 HOH HOH . U 11 HOH C 18 618 34 HOH HOH . U 11 HOH C 19 619 17 HOH HOH . U 11 HOH C 20 620 12 HOH HOH . U 11 HOH C 21 621 47 HOH HOH . U 11 HOH C 22 622 84 HOH HOH . U 11 HOH C 23 623 28 HOH HOH . U 11 HOH C 24 624 5 HOH HOH . U 11 HOH C 25 625 75 HOH HOH . U 11 HOH C 26 626 8 HOH HOH . U 11 HOH C 27 627 38 HOH HOH . U 11 HOH C 28 628 20 HOH HOH . U 11 HOH C 29 629 65 HOH HOH . U 11 HOH C 30 630 21 HOH HOH . U 11 HOH C 31 631 19 HOH HOH . U 11 HOH C 32 632 31 HOH HOH . U 11 HOH C 33 633 54 HOH HOH . U 11 HOH C 34 634 56 HOH HOH . U 11 HOH C 35 635 14 HOH HOH . U 11 HOH C 36 636 43 HOH HOH . U 11 HOH C 37 637 42 HOH HOH . U 11 HOH C 38 638 66 HOH HOH . U 11 HOH C 39 639 53 HOH HOH . U 11 HOH C 40 640 27 HOH HOH . U 11 HOH C 41 641 51 HOH HOH . U 11 HOH C 42 642 13 HOH HOH . U 11 HOH C 43 643 7 HOH HOH . U 11 HOH C 44 644 18 HOH HOH . U 11 HOH C 45 645 69 HOH HOH . U 11 HOH C 46 646 68 HOH HOH . V 11 HOH D 1 601 81 HOH HOH . V 11 HOH D 2 602 62 HOH HOH . V 11 HOH D 3 603 79 HOH HOH . V 11 HOH D 4 604 82 HOH HOH . W 11 HOH E 1 201 61 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 PG ACP . . . R 10 -7.687 -49.457 93.389 1 99.39 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . R 10 -7.062 -48.681 94.48 1 103.54 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . R 10 -6.692 -50.659 93.025 1 104.84 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . R 10 -7.916 -48.526 92.093 1 100.95 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . R 10 -10.284 -48.966 94.785 1 90 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . R 10 -11.274 -48.434 93.814 1 86.93 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . R 10 -9.369 -47.743 95.29 1 83.89 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . R 10 -9.263 -50.178 93.918 1 94.43 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . R 10 -10.402 -50.268 97.405 1 85.78 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . R 10 -9.329 -51.291 97.082 1 88.41 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . R 10 -11.562 -50.672 98.295 1 75.19 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . R 10 -11.05 -49.655 96.038 1 86.42 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . R 10 -9.629 -49.099 98.199 1 79.71 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . R 10 -9.405 -49.398 99.57 1 76.17 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . R 10 -8.608 -48.353 100.329 1 74.67 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . R 10 -9.217 -48.323 101.623 1 70.88 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . R 10 -7.137 -48.728 100.518 1 74.01 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . R 10 -6.248 -47.624 100.289 1 69.9 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . R 10 -7.065 -49.271 101.946 1 73.02 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . R 10 -6.053 -48.684 102.767 1 79.4 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . R 10 -8.409 -48.998 102.588 1 67.39 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . R 10 -8.94 -50.303 103.024 1 63.95 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . R 10 -9.826 -51.103 102.411 1 62.87 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . R 10 -10.041 -52.224 103.147 1 62.61 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . R 10 -9.279 -52.168 104.244 1 62.97 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . R 10 -9.02 -53.019 105.437 1 67.46 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . R 10 -9.632 -54.213 105.637 1 68.47 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . R 10 -8.14 -52.554 106.352 1 72.1 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . R 10 -7.51 -51.369 106.2 1 72.01 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . R 10 -7.696 -50.556 105.136 1 68.81 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . R 10 -8.555 -50.894 104.148 1 65.5 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #