data_5XKF
#
_model_server_result.job_id            YoaGviUXD6oLfIa8jsqsyA 
_model_server_result.datetime_utc      '2024-10-20 19:55:34' 
_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          5xkf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":502}' 
#
_entry.id    5XKF 
#
_exptl.entry_id    5XKF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              24.305 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MAGNESIUM ION' 
_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            5XKF 
_cell.length_a            105.617 
_cell.length_b            158.572 
_cell.length_c            182.245 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XKF 
_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,X,Y 
_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
? 6 H N N 
? 6 L N N 
? 6 P N N 
? 6 S 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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? 
metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? 
metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc10 H MG MG . A MG 502 1_555 U O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc11 H MG MG . A MG 502 1_555 U O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc12 H MG MG . A MG 502 1_555 U O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc13 H MG MG . A MG 502 1_555 V O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc16 L MG MG . B MG 502 1_555 V O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc17 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc18 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? 
metalc ? metalc19 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? 
metalc ? metalc20 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc21 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
metalc ? metalc22 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc23 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc24 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc25 P MG MG . C MG 502 1_555 W O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc26 P MG MG . C MG 502 1_555 W O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc27 P MG MG . C MG 502 1_555 W O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc28 P MG MG . C MG 502 1_555 W O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc29 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc30 R O1B GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc31 S MG MG . D MG 502 1_555 X O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
#
_chem_comp.formula           'Mg 2' 
_chem_comp.formula_weight    24.305 
_chem_comp.id                MG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MAGNESIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5XKF 
_atom_sites.fract_transf_matrix[1][1]    0.009468 
_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]    0.006306 
_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]    0.005487 
_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 GOL A 1 504 601 GOL GOL . 
K 9 GDP B 1 501 501 GDP GDP . 
L 6 MG B 1 502 502 MG MG . 
M 10 MES B 1 503 505 MES MES . 
N 11 88U B 1 504 2 88U M68 . 
O 5 GTP C 1 501 501 GTP GTP . 
P 6 MG C 1 502 502 MG MG . 
Q 7 CA C 1 503 504 CA CA . 
R 5 GTP D 1 501 501 GTP GTP . 
S 6 MG D 1 502 502 MG MG . 
T 11 88U D 1 503 1 88U M68 . 
U 12 HOH A 1 601 17 HOH HOH . 
U 12 HOH A 2 602 6 HOH HOH . 
U 12 HOH A 3 603 8 HOH HOH . 
U 12 HOH A 4 604 9 HOH HOH . 
V 12 HOH B 1 601 20 HOH HOH . 
V 12 HOH B 2 602 19 HOH HOH . 
V 12 HOH B 3 603 18 HOH HOH . 
V 12 HOH B 4 604 22 HOH HOH . 
V 12 HOH B 5 605 7 HOH HOH . 
V 12 HOH B 6 606 10 HOH HOH . 
V 12 HOH B 7 607 13 HOH HOH . 
V 12 HOH B 8 608 11 HOH HOH . 
V 12 HOH B 9 609 21 HOH HOH . 
V 12 HOH B 10 610 28 HOH HOH . 
V 12 HOH B 11 611 16 HOH HOH . 
W 12 HOH C 1 601 24 HOH HOH . 
W 12 HOH C 2 602 4 HOH HOH . 
W 12 HOH C 3 603 2 HOH HOH . 
W 12 HOH C 4 604 3 HOH HOH . 
W 12 HOH C 5 605 1 HOH HOH . 
W 12 HOH C 6 606 30 HOH HOH . 
W 12 HOH C 7 607 29 HOH HOH . 
W 12 HOH C 8 608 26 HOH HOH . 
W 12 HOH C 9 609 23 HOH HOH . 
W 12 HOH C 10 610 27 HOH HOH . 
W 12 HOH C 11 611 12 HOH HOH . 
X 12 HOH D 1 601 15 HOH HOH . 
X 12 HOH D 2 602 5 HOH HOH . 
X 12 HOH D 3 603 14 HOH HOH . 
X 12 HOH D 4 604 25 HOH HOH . 
Y 12 HOH E 1 201 31 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           MG 
_atom_site.label_atom_id         MG 
_atom_site.label_comp_id         MG 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         S 
_atom_site.label_entity_id       6 
_atom_site.Cartn_x               24.752 
_atom_site.Cartn_y               307.932 
_atom_site.Cartn_z               -47.422 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        72.67 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          MG 
_atom_site.auth_comp_id          MG 
_atom_site.auth_seq_id           502 
_atom_site.auth_asym_id          D 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    58 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           1 
#