data_3QI2
#
_model_server_result.job_id            VDGX5dRTATVv5QPFLhHwtA 
_model_server_result.datetime_utc      '2024-10-11 00:27:36' 
_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          3qi2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":356}' 
#
_entry.id    3QI2 
#
_exptl.entry_id    3QI2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            3QI2 
_cell.length_a            70.003 
_cell.length_b            131.018 
_cell.length_c            203.307 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QI2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,C,E,F,G,J,L 1 1 
B,D,H,I,K,M 2 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
? 3 E N N 
? 3 H N N 
#
_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                     3QI2 
_atom_sites.fract_transf_matrix[1][1]    0.014285 
_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]    0.007633 
_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]    0.004919 
_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 3 GDP A 1 355 355 GDP GDP . 
F 4 SO4 A 1 2 2 SO4 SO4 . 
G 5 GOL A 1 3 3 GOL GOL . 
H 3 GDP B 1 356 356 GDP GDP . 
I 4 SO4 B 1 1 1 SO4 SO4 . 
J 6 HOH A 1 4 4 HOH HOH . 
J 6 HOH A 2 6 6 HOH HOH . 
J 6 HOH A 3 7 7 HOH HOH . 
J 6 HOH A 4 8 8 HOH HOH . 
J 6 HOH A 5 12 12 HOH HOH . 
J 6 HOH A 6 14 14 HOH HOH . 
J 6 HOH A 7 15 15 HOH HOH . 
J 6 HOH A 8 17 17 HOH HOH . 
J 6 HOH A 9 19 19 HOH HOH . 
J 6 HOH A 10 20 20 HOH HOH . 
J 6 HOH A 11 25 25 HOH HOH . 
J 6 HOH A 12 356 3 HOH HOH . 
J 6 HOH A 13 357 27 HOH HOH . 
J 6 HOH A 14 358 29 HOH HOH . 
J 6 HOH A 15 359 31 HOH HOH . 
J 6 HOH A 16 360 33 HOH HOH . 
J 6 HOH A 17 361 35 HOH HOH . 
J 6 HOH A 18 362 36 HOH HOH . 
J 6 HOH A 19 363 38 HOH HOH . 
K 6 HOH B 1 2 2 HOH HOH . 
K 6 HOH B 2 5 5 HOH HOH . 
K 6 HOH B 3 10 10 HOH HOH . 
K 6 HOH B 4 11 11 HOH HOH . 
K 6 HOH B 5 13 13 HOH HOH . 
K 6 HOH B 6 16 16 HOH HOH . 
K 6 HOH B 7 18 18 HOH HOH . 
K 6 HOH B 8 21 21 HOH HOH . 
K 6 HOH B 9 26 26 HOH HOH . 
K 6 HOH B 10 355 1 HOH HOH . 
K 6 HOH B 11 357 28 HOH HOH . 
K 6 HOH B 12 358 34 HOH HOH . 
K 6 HOH B 13 359 39 HOH HOH . 
L 6 HOH C 1 22 22 HOH HOH . 
L 6 HOH C 2 32 32 HOH HOH . 
M 6 HOH D 1 9 9 HOH HOH . 
M 6 HOH D 2 30 30 HOH HOH . 
M 6 HOH D 3 37 37 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 . . . H 3 -20.142 50.441 17.163 1 49.49 ? PB GDP 356 B 1 
HETATM 2 O O1B GDP . . . H 3 -20.795 49.231 16.538 1 47.63 ? O1B GDP 356 B 1 
HETATM 3 O O2B GDP . . . H 3 -19.464 50.035 18.45 1 71.23 ? O2B GDP 356 B 1 
HETATM 4 O O3B GDP . . . H 3 -19.122 51.013 16.206 1 22.85 ? O3B GDP 356 B 1 
HETATM 5 O O3A GDP . . . H 3 -21.252 51.558 17.486 1 105.21 ? O3A GDP 356 B 1 
HETATM 6 P PA GDP . . . H 3 -21.946 52.365 16.282 1 47.23 ? PA GDP 356 B 1 
HETATM 7 O O1A GDP . . . H 3 -23.245 51.714 15.881 1 44.08 ? O1A GDP 356 B 1 
HETATM 8 O O2A GDP . . . H 3 -21.014 52.476 15.105 1 43.26 ? O2A GDP 356 B 1 
HETATM 9 O O5' GDP . . . H 3 -22.223 53.813 16.92 1 63.56 ? O5' GDP 356 B 1 
HETATM 10 C C5' GDP . . . H 3 -21.807 54.979 16.22 1 47.41 ? C5' GDP 356 B 1 
HETATM 11 C C4' GDP . . . H 3 -22.751 56.119 16.555 1 48.76 ? C4' GDP 356 B 1 
HETATM 12 O O4' GDP . . . H 3 -22.44 57.211 15.694 1 66.05 ? O4' GDP 356 B 1 
HETATM 13 C C3' GDP . . . H 3 -24.183 55.711 16.279 1 41.78 ? C3' GDP 356 B 1 
HETATM 14 O O3' GDP . . . H 3 -25.014 56.176 17.344 1 46.34 ? O3' GDP 356 B 1 
HETATM 15 C C2' GDP . . . H 3 -24.561 56.4 14.984 1 59.2 ? C2' GDP 356 B 1 
HETATM 16 O O2' GDP . . . H 3 -25.862 56.984 15.083 1 68.34 ? O2' GDP 356 B 1 
HETATM 17 C C1' GDP . . . H 3 -23.511 57.48 14.786 1 62.9 ? C1' GDP 356 B 1 
HETATM 18 N N9 GDP . . . H 3 -22.968 57.435 13.408 1 52.6 ? N9 GDP 356 B 1 
HETATM 19 C C8 GDP . . . H 3 -22.419 56.358 12.814 1 49.56 ? C8 GDP 356 B 1 
HETATM 20 N N7 GDP . . . H 3 -22.004 56.654 11.555 1 43.82 ? N7 GDP 356 B 1 
HETATM 21 C C5 GDP . . . H 3 -22.279 57.953 11.337 1 38.32 ? C5 GDP 356 B 1 
HETATM 22 C C6 GDP . . . H 3 -22.101 58.908 10.221 1 44.5 ? C6 GDP 356 B 1 
HETATM 23 O O6 GDP . . . H 3 -21.572 58.545 9.149 1 52.66 ? O6 GDP 356 B 1 
HETATM 24 N N1 GDP . . . H 3 -22.524 60.166 10.398 1 38.14 ? N1 GDP 356 B 1 
HETATM 25 C C2 GDP . . . H 3 -23.097 60.579 11.545 1 40.31 ? C2 GDP 356 B 1 
HETATM 26 N N2 GDP . . . H 3 -23.498 61.869 11.645 1 53.04 ? N2 GDP 356 B 1 
HETATM 27 N N3 GDP . . . H 3 -23.291 59.76 12.608 1 34.64 ? N3 GDP 356 B 1 
HETATM 28 C C4 GDP . . . H 3 -22.91 58.463 12.562 1 39.37 ? C4 GDP 356 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#