data_8ALK # _model_server_result.job_id R2rNpM-fqcdFM6b39aO1bA _model_server_result.datetime_utc '2025-02-05 09:57:38' _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 8alk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 8ALK # _exptl.entry_id 8ALK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 8ALK _cell.length_a 119.332 _cell.length_b 119.332 _cell.length_c 79.058 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ALK _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _symmetry.space_group_name_H-M 'P 61' # _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 _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 4 _struct_asym.id F _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 covale ? covale1 A SG CYS 374 A CYS 391 1_555 H C37 OJU . B OJU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B OG1 THR 77 B THR 76 1_555 H P OJU . B OJU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 A OD1 ASP 88 A ASP 105 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? metalc ? metalc2 A OD2 ASP 88 A ASP 105 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc3 A OD1 ASP 88 A ASP 105 1_555 D CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc4 A O GLY 89 A GLY 106 1_555 D CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc5 A OD2 ASP 173 A ASP 190 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc6 A OD1 ASP 237 A ASP 254 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc7 A OD2 ASP 237 A ASP 254 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc8 A OD2 ASP 377 A ASP 394 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc9 C CA CA . A CA 501 1_555 I O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc10 C CA CA . A CA 501 1_555 I O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc11 C CA CA . A CA 501 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc12 D CA CA . A CA 502 1_555 I O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc13 D CA CA . A CA 502 1_555 I O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc14 D CA CA . A CA 502 1_555 I O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc15 D CA CA . A CA 502 1_555 H O3 OJU . B OJU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc16 E CA CA . A CA 503 1_555 I O HOH . A HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc17 E CA CA . A CA 503 1_555 I O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc18 E CA CA . A CA 503 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc19 B OG SER 23 B SER 22 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc20 B OD1 ASP 45 B ASP 44 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc21 B OD2 ASP 64 B ASP 63 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc22 F O1B GDP . B GDP 201 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc23 G CA CA . B CA 202 1_555 J O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc24 G CA CA . B CA 202 1_555 J O HOH . B HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc25 G CA CA . B CA 202 1_555 J O HOH . B HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 8ALK _atom_sites.fract_transf_matrix[1][1] 0.00838 _atom_sites.fract_transf_matrix[1][2] 0.004838 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009676 _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] 0.012649 _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 CA A 1 501 1 CA CA . D 3 CA A 1 502 8 CA CA . E 3 CA A 1 503 9 CA CA . F 4 GDP B 1 201 201 GDP GDP . G 3 CA B 1 202 6 CA CA . H 5 OJU B 1 203 502 OJU PCX . I 6 HOH A 1 601 82 HOH HOH . I 6 HOH A 2 602 1 HOH HOH . I 6 HOH A 3 603 23 HOH HOH . I 6 HOH A 4 604 61 HOH HOH . I 6 HOH A 5 605 73 HOH HOH . I 6 HOH A 6 606 70 HOH HOH . I 6 HOH A 7 607 60 HOH HOH . I 6 HOH A 8 608 9 HOH HOH . I 6 HOH A 9 609 17 HOH HOH . I 6 HOH A 10 610 3 HOH HOH . I 6 HOH A 11 611 4 HOH HOH . I 6 HOH A 12 612 57 HOH HOH . I 6 HOH A 13 613 43 HOH HOH . I 6 HOH A 14 614 79 HOH HOH . I 6 HOH A 15 615 15 HOH HOH . I 6 HOH A 16 616 18 HOH HOH . I 6 HOH A 17 617 44 HOH HOH . I 6 HOH A 18 618 84 HOH HOH . I 6 HOH A 19 619 85 HOH HOH . I 6 HOH A 20 620 26 HOH HOH . I 6 HOH A 21 621 81 HOH HOH . I 6 HOH A 22 622 41 HOH HOH . I 6 HOH A 23 623 7 HOH HOH . I 6 HOH A 24 624 59 HOH HOH . I 6 HOH A 25 625 62 HOH HOH . I 6 HOH A 26 626 5 HOH HOH . I 6 HOH A 27 627 20 HOH HOH . I 6 HOH A 28 628 63 HOH HOH . I 6 HOH A 29 629 8 HOH HOH . I 6 HOH A 30 630 78 HOH HOH . I 6 HOH A 31 631 29 HOH HOH . I 6 HOH A 32 632 10 HOH HOH . I 6 HOH A 33 633 38 HOH HOH . I 6 HOH A 34 634 13 HOH HOH . I 6 HOH A 35 635 19 HOH HOH . I 6 HOH A 36 636 2 HOH HOH . I 6 HOH A 37 637 51 HOH HOH . I 6 HOH A 38 638 11 HOH HOH . I 6 HOH A 39 639 12 HOH HOH . I 6 HOH A 40 640 16 HOH HOH . I 6 HOH A 41 641 36 HOH HOH . I 6 HOH A 42 642 28 HOH HOH . I 6 HOH A 43 643 66 HOH HOH . I 6 HOH A 44 644 47 HOH HOH . I 6 HOH A 45 645 34 HOH HOH . I 6 HOH A 46 646 32 HOH HOH . I 6 HOH A 47 647 54 HOH HOH . I 6 HOH A 48 648 64 HOH HOH . I 6 HOH A 49 649 22 HOH HOH . I 6 HOH A 50 650 14 HOH HOH . I 6 HOH A 51 651 67 HOH HOH . I 6 HOH A 52 652 48 HOH HOH . I 6 HOH A 53 653 25 HOH HOH . I 6 HOH A 54 654 45 HOH HOH . I 6 HOH A 55 655 31 HOH HOH . I 6 HOH A 56 656 21 HOH HOH . I 6 HOH A 57 657 33 HOH HOH . I 6 HOH A 58 658 50 HOH HOH . I 6 HOH A 59 659 30 HOH HOH . I 6 HOH A 60 660 68 HOH HOH . I 6 HOH A 61 661 80 HOH HOH . J 6 HOH B 1 301 83 HOH HOH . J 6 HOH B 2 302 27 HOH HOH . J 6 HOH B 3 303 42 HOH HOH . J 6 HOH B 4 304 6 HOH HOH . J 6 HOH B 5 305 65 HOH HOH . J 6 HOH B 6 306 35 HOH HOH . J 6 HOH B 7 307 56 HOH HOH . J 6 HOH B 8 308 72 HOH HOH . J 6 HOH B 9 309 69 HOH HOH . J 6 HOH B 10 310 40 HOH HOH . J 6 HOH B 11 311 58 HOH HOH . J 6 HOH B 12 312 24 HOH HOH . J 6 HOH B 13 313 74 HOH HOH . J 6 HOH B 14 314 46 HOH HOH . J 6 HOH B 15 315 49 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 PB GDP . . . F 4 -57.275 -23.611 -24.01 1 54.41 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . F 4 -56.241 -22.515 -23.937 1 52.54 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . F 4 -56.682 -24.965 -23.709 1 54.28 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . F 4 -58.367 -23.301 -23.004 1 53.01 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . F 4 -57.99 -23.598 -25.447 1 49.91 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . F 4 -57.223 -23.194 -26.797 1 59 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . F 4 -57.175 -21.688 -26.934 1 50.41 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . F 4 -55.842 -23.804 -26.865 1 64.88 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . F 4 -58.184 -23.837 -27.917 1 64.21 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . F 4 -57.628 -24.26 -29.155 1 86.11 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . F 4 -58.696 -24.927 -30.005 1 65.26 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . F 4 -59.982 -24.398 -29.668 1 58.9 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . F 4 -58.421 -24.599 -31.459 1 71.66 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . F 4 -58.341 -25.809 -32.217 1 89.22 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . F 4 -59.589 -23.751 -31.919 1 73.24 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . F 4 -60.086 -24.229 -33.173 1 89.27 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . F 4 -60.641 -23.888 -30.827 1 62.29 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . F 4 -61.275 -22.577 -30.526 1 64.63 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . F 4 -60.883 -21.697 -29.585 1 56.33 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . F 4 -61.685 -20.599 -29.574 1 54.26 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . F 4 -62.619 -20.771 -30.529 1 58.38 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . F 4 -63.775 -20.001 -31.053 1 56.17 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . F 4 -64.076 -18.885 -30.574 1 52.29 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . F 4 -64.489 -20.534 -32.054 1 56.1 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . F 4 -64.191 -21.736 -32.586 1 62.84 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . F 4 -64.961 -22.211 -33.593 1 59.94 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . F 4 -63.149 -22.496 -32.157 1 65.32 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . F 4 -62.344 -22.075 -31.152 1 65.9 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #