data_6JSJ
#
_model_server_result.job_id            HoXoJgVRpGY1MRjuhk41KQ 
_model_server_result.datetime_utc      '2024-10-25 20:37:04' 
_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          6jsj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":701}' 
#
_entry.id    6JSJ 
#
_exptl.entry_id    6JSJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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         90 
_cell.entry_id            6JSJ 
_cell.length_a            152.94 
_cell.length_b            152.94 
_cell.length_c            236.15 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JSJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,Z,AA,BA,CA,DA,EA 
_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
? 2 D N N 
? 2 N N N 
? 2 Y 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
disulf ? disulf1 A SG CYS 594 A CYS 594 1_555 A SG CYS 603 A CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 594 B CYS 594 1_555 B SG CYS 603 B CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 C SG CYS 594 C CYS 594 1_555 C SG CYS 603 C CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
#
_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     ? 
#
_atom_sites.entry_id                     6JSJ 
_atom_sites.fract_transf_matrix[1][1]    0.006539 
_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]    0.006539 
_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]    0.004235 
_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
D 2 GDP A 1 701 700 GDP GDP . 
E 3 IOD A 1 702 711 IOD IOD . 
F 3 IOD A 1 703 712 IOD IOD . 
G 3 IOD A 1 704 713 IOD IOD . 
H 3 IOD A 1 705 714 IOD IOD . 
I 3 IOD A 1 706 1 IOD IOD . 
J 3 IOD A 1 707 2 IOD IOD . 
K 3 IOD A 1 708 3 IOD IOD . 
L 3 IOD A 1 709 4 IOD IOD . 
M 3 IOD A 1 710 5 IOD IOD . 
N 2 GDP B 1 701 700 GDP GDP . 
O 3 IOD B 1 702 711 IOD IOD . 
P 3 IOD B 1 703 712 IOD IOD . 
Q 3 IOD B 1 704 713 IOD IOD . 
R 3 IOD B 1 705 714 IOD IOD . 
S 3 IOD B 1 706 6 IOD IOD . 
T 3 IOD B 1 707 7 IOD IOD . 
U 3 IOD B 1 708 9 IOD IOD . 
V 3 IOD B 1 709 10 IOD IOD . 
W 3 IOD B 1 710 13 IOD IOD . 
X 3 IOD B 1 711 14 IOD IOD . 
Y 2 GDP C 1 701 700 GDP GDP . 
Z 3 IOD C 1 702 711 IOD IOD . 
AA 3 IOD C 1 703 712 IOD IOD . 
BA 3 IOD C 1 704 713 IOD IOD . 
CA 3 IOD C 1 705 714 IOD IOD . 
DA 3 IOD C 1 706 11 IOD IOD . 
EA 3 IOD C 1 707 12 IOD IOD . 
#
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 . . . N 2 -15.887 120.292 277.07 1 139.9 ? PB GDP 701 B 1 
HETATM 2 O O1B GDP . . . N 2 -16.129 121.552 276.334 1 141.02 ? O1B GDP 701 B 1 
HETATM 3 O O2B GDP . . . N 2 -16.014 120.395 278.541 1 140.33 -1 O2B GDP 701 B 1 
HETATM 4 O O3B GDP . . . N 2 -14.739 119.493 276.585 1 140.35 ? O3B GDP 701 B 1 
HETATM 5 O O3A GDP . . . N 2 -17.163 119.378 276.705 1 137.21 ? O3A GDP 701 B 1 
HETATM 6 P PA GDP . . . N 2 -17.55 118.908 275.207 1 135.81 ? PA GDP 701 B 1 
HETATM 7 O O1A GDP . . . N 2 -16.4 119.075 274.281 1 135.34 ? O1A GDP 701 B 1 
HETATM 8 O O2A GDP . . . N 2 -18.826 119.549 274.869 1 134.33 -1 O2A GDP 701 B 1 
HETATM 9 O O5' GDP . . . N 2 -17.873 117.336 275.471 1 136.08 ? O5' GDP 701 B 1 
HETATM 10 C C5' GDP . . . N 2 -17.093 116.271 274.898 1 134.46 ? C5' GDP 701 B 1 
HETATM 11 C C4' GDP . . . N 2 -18.001 115.187 274.308 1 132.11 ? C4' GDP 701 B 1 
HETATM 12 O O4' GDP . . . N 2 -19.193 115.034 275.095 1 130.63 ? O4' GDP 701 B 1 
HETATM 13 C C3' GDP . . . N 2 -18.444 115.584 272.9 1 132.07 ? C3' GDP 701 B 1 
HETATM 14 O O3' GDP . . . N 2 -17.916 114.629 271.965 1 132.08 ? O3' GDP 701 B 1 
HETATM 15 C C2' GDP . . . N 2 -19.98 115.562 272.959 1 131.98 ? C2' GDP 701 B 1 
HETATM 16 O O2' GDP . . . N 2 -20.612 114.968 271.799 1 132.28 ? O2' GDP 701 B 1 
HETATM 17 C C1' GDP . . . N 2 -20.253 114.717 274.174 1 130.58 ? C1' GDP 701 B 1 
HETATM 18 N N9 GDP . . . N 2 -21.499 115.119 274.851 1 129.44 ? N9 GDP 701 B 1 
HETATM 19 C C8 GDP . . . N 2 -21.808 116.337 275.303 1 129.66 ? C8 GDP 701 B 1 
HETATM 20 N N7 GDP . . . N 2 -22.982 116.263 275.915 1 129.61 ? N7 GDP 701 B 1 
HETATM 21 C C5 GDP . . . N 2 -23.387 114.995 275.873 1 128.66 ? C5 GDP 701 B 1 
HETATM 22 C C6 GDP . . . N 2 -24.48 114.38 276.341 1 127.33 ? C6 GDP 701 B 1 
HETATM 23 O O6 GDP . . . N 2 -25.386 115.145 277.006 1 125.77 ? O6 GDP 701 B 1 
HETATM 24 N N1 GDP . . . N 2 -24.655 113.059 276.169 1 127.57 ? N1 GDP 701 B 1 
HETATM 25 C C2 GDP . . . N 2 -23.723 112.33 275.525 1 127.56 ? C2 GDP 701 B 1 
HETATM 26 N N2 GDP . . . N 2 -23.901 111.019 275.353 1 126.67 ? N2 GDP 701 B 1 
HETATM 27 N N3 GDP . . . N 2 -22.623 112.95 275.044 1 128.04 ? N3 GDP 701 B 1 
HETATM 28 C C4 GDP . . . N 2 -22.46 114.281 275.219 1 128.55 ? C4 GDP 701 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#