data_4GVL # _model_server_result.job_id 74KHgFb1CLMqCzo0xfixmg _model_server_result.datetime_utc '2025-01-05 08:20:59' _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 4gvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":602}' # _entry.id 4GVL # _exptl.entry_id 4GVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 90 _cell.entry_id 4GVL _cell.length_a 110.648 _cell.length_b 161.693 _cell.length_c 310.127 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA octameric 8 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_645 -x+1,-y-1,z -1 0 0 0 -1 0 0 0 1 110.648 -161.693 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 J N N ? 3 M N N ? 3 P 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 O THR 77 A THR 183 1_555 H CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc2 A OD1 ASN 104 A ASN 210 1_555 H CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc3 A OG1 THR 108 A THR 214 1_555 H CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc4 A NE2 HIS 253 A HIS 359 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc5 A SG CYS 258 A CYS 364 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc6 A SG CYS 282 A CYS 388 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc7 A ND1 HIS 285 A HIS 391 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? metalc ? metalc8 A O GLU 343 A GLU 449 1_555 G CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc9 A OD1 ASN 344 A ASN 450 1_555 G CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc10 A OE1 GLN 347 A GLN 453 1_555 G CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc11 G CA CA . A CA 603 1_555 B O THR 77 B THR 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc12 G CA CA . A CA 603 1_555 B OD1 ASN 104 B ASN 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc13 G CA CA . A CA 603 1_555 B OG1 THR 108 B THR 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc14 H CA CA . A CA 604 1_555 D O GLU 343 D GLU 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc15 H CA CA . A CA 604 1_555 D OE1 GLN 347 D GLN 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.061 ? metalc ? metalc16 B NE2 HIS 253 B HIS 359 1_555 I ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc17 B SG CYS 258 B CYS 364 1_555 I ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc18 B SG CYS 282 B CYS 388 1_555 I ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc19 B ND1 HIS 285 B HIS 391 1_555 I ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc20 B O GLU 343 B GLU 449 1_555 K CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc21 B OD1 ASN 344 B ASN 450 1_555 K CA CA . B CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc22 K CA CA . B CA 603 1_555 C O THR 77 C THR 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc23 K CA CA . B CA 603 1_555 C OD1 ASN 104 C ASN 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc24 K CA CA . B CA 603 1_555 C OG1 THR 108 C THR 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc25 C NE2 HIS 253 C HIS 359 1_555 L ZN ZN . C ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc26 C SG CYS 258 C CYS 364 1_555 L ZN ZN . C ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc27 C SG CYS 282 C CYS 388 1_555 L ZN ZN . C ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc28 C ND1 HIS 285 C HIS 391 1_555 L ZN ZN . C ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc29 C O GLU 343 C GLU 449 1_555 N CA CA . C CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc30 C OD1 ASN 344 C ASN 450 1_555 N CA CA . C CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc31 C OE1 GLN 347 C GLN 453 1_555 N CA CA . C CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc32 N CA CA . C CA 603 1_555 D O THR 77 D THR 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc33 N CA CA . C CA 603 1_555 D OD1 ASN 104 D ASN 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? metalc ? metalc34 N CA CA . C CA 603 1_555 D OG1 THR 108 D THR 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc35 D NE2 HIS 253 D HIS 359 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc36 D SG CYS 258 D CYS 364 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc37 D SG CYS 282 D CYS 388 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc38 D ND1 HIS 285 D HIS 391 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 4GVL _atom_sites.fract_transf_matrix[1][1] 0.009038 _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] 0.006185 _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] 0.003224 _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 E 2 ZN A 1 601 601 ZN ZN . F 3 AMP A 1 602 602 AMP AMP . G 4 CA A 1 603 603 CA CA . H 4 CA A 1 604 603 CA CA . I 2 ZN B 1 601 601 ZN ZN . J 3 AMP B 1 602 602 AMP AMP . K 4 CA B 1 603 603 CA CA . L 2 ZN C 1 601 601 ZN ZN . M 3 AMP C 1 602 602 AMP AMP . N 4 CA C 1 603 603 CA CA . O 2 ZN D 1 601 601 ZN ZN . P 3 AMP D 1 602 602 AMP AMP . # 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 AMP . . . M 3 50.878 -37.998 -34.885 1 166.09 ? P AMP 602 C 1 HETATM 2 O O1P AMP . . . M 3 50.653 -36.633 -35.485 1 168.11 ? O1P AMP 602 C 1 HETATM 3 O O2P AMP . . . M 3 50.204 -38.161 -33.547 1 165.4 ? O2P AMP 602 C 1 HETATM 4 O O3P AMP . . . M 3 52.304 -38.501 -34.965 1 164.51 ? O3P AMP 602 C 1 HETATM 5 O O5' AMP . . . M 3 50.047 -38.99 -35.848 1 167.32 ? O5' AMP 602 C 1 HETATM 6 C C5' AMP . . . M 3 49.932 -40.389 -35.576 1 166.52 ? C5' AMP 602 C 1 HETATM 7 C C4' AMP . . . M 3 49.891 -41.159 -36.891 1 168.1 ? C4' AMP 602 C 1 HETATM 8 O O4' AMP . . . M 3 50.17 -42.544 -36.67 1 167.46 ? O4' AMP 602 C 1 HETATM 9 C C3' AMP . . . M 3 48.524 -41.088 -37.559 1 171.07 ? C3' AMP 602 C 1 HETATM 10 O O3' AMP . . . M 3 48.664 -40.475 -38.844 1 172.94 ? O3' AMP 602 C 1 HETATM 11 C C2' AMP . . . M 3 48.065 -42.529 -37.695 1 172.27 ? C2' AMP 602 C 1 HETATM 12 O O2' AMP . . . M 3 47.453 -42.786 -38.964 1 176.4 ? O2' AMP 602 C 1 HETATM 13 C C1' AMP . . . M 3 49.353 -43.321 -37.55 1 170.21 ? C1' AMP 602 C 1 HETATM 14 N N9 AMP . . . M 3 49.157 -44.709 -37.051 1 170.12 ? N9 AMP 602 C 1 HETATM 15 C C8 AMP . . . M 3 48.21 -45.151 -36.197 1 170.13 ? C8 AMP 602 C 1 HETATM 16 N N7 AMP . . . M 3 48.338 -46.485 -35.967 1 170.43 ? N7 AMP 602 C 1 HETATM 17 C C5 AMP . . . M 3 49.391 -46.922 -36.689 1 170.83 ? C5 AMP 602 C 1 HETATM 18 C C6 AMP . . . M 3 50.088 -48.222 -36.916 1 171.78 ? C6 AMP 602 C 1 HETATM 19 N N6 AMP . . . M 3 49.675 -49.363 -36.308 1 172.36 ? N6 AMP 602 C 1 HETATM 20 N N1 AMP . . . M 3 51.156 -48.231 -37.756 1 172.52 ? N1 AMP 602 C 1 HETATM 21 C C2 AMP . . . M 3 51.591 -47.111 -38.373 1 172.2 ? C2 AMP 602 C 1 HETATM 22 N N3 AMP . . . M 3 51.007 -45.904 -38.217 1 171.1 ? N3 AMP 602 C 1 HETATM 23 C C4 AMP . . . M 3 49.925 -45.745 -37.404 1 170.57 ? C4 AMP 602 C 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #