data_5TC3
#
_model_server_result.job_id            4_xazfu-mMRv32XRCbUbyg 
_model_server_result.datetime_utc      '2024-11-18 05:54:44' 
_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          5tc3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":602}' 
#
_entry.id    5TC3 
#
_exptl.entry_id    5TC3 
_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    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            5TC3 
_cell.length_a            147.88 
_cell.length_b            147.88 
_cell.length_c            103.542 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5TC3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
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 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M 1 2 
A,B,C,D,E,F,G,H,I,J,K,L,M 1 3 
A,B,C,D,E,F,G,H,I,J,K,L,M 1 4 
#
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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 F N N 
? 4 J N N 
? 4 K 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 178 n n 
PB O2B GDP sing 179 n n 
PB O3B GDP sing 180 n n 
PB O3A GDP sing 181 n n 
O2B HOB2 GDP sing 182 n n 
O3B HOB3 GDP sing 183 n n 
O3A PA GDP sing 184 n n 
PA O1A GDP doub 185 n n 
PA O2A GDP sing 186 n n 
PA O5' GDP sing 187 n n 
O2A HOA2 GDP sing 188 n n 
O5' C5' GDP sing 189 n n 
C5' C4' GDP sing 190 n n 
C5' H5' GDP sing 191 n n 
C5' "H5''" GDP sing 192 n n 
C4' O4' GDP sing 193 n n 
C4' C3' GDP sing 194 n n 
C4' H4' GDP sing 195 n n 
O4' C1' GDP sing 196 n n 
C3' O3' GDP sing 197 n n 
C3' C2' GDP sing 198 n n 
C3' H3' GDP sing 199 n n 
O3' HO3' GDP sing 200 n n 
C2' O2' GDP sing 201 n n 
C2' C1' GDP sing 202 n n 
C2' H2' GDP sing 203 n n 
O2' HO2' GDP sing 204 n n 
C1' N9 GDP sing 205 n n 
C1' H1' GDP sing 206 n n 
N9 C8 GDP sing 207 n y 
N9 C4 GDP sing 208 n y 
C8 N7 GDP doub 209 n y 
C8 H8 GDP sing 210 n n 
N7 C5 GDP sing 211 n y 
C5 C6 GDP sing 212 n n 
C5 C4 GDP doub 213 n y 
C6 O6 GDP doub 214 n n 
C6 N1 GDP sing 215 n n 
N1 C2 GDP sing 216 n n 
N1 HN1 GDP sing 217 n n 
C2 N2 GDP sing 218 n n 
C2 N3 GDP doub 219 n n 
N2 HN21 GDP sing 220 n n 
N2 HN22 GDP sing 221 n n 
N3 C4 GDP sing 222 n n 
#
_atom_sites.entry_id                     5TC3 
_atom_sites.fract_transf_matrix[1][1]    0.006762 
_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]    0.006762 
_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]    0.009658 
_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 2 5GP A 1 600 600 5GP 5GP . 
D 3 ATP A 1 601 601 ATP ATP . 
E 4 GDP A 1 602 602 GDP GDP . 
F 4 GDP A 1 603 603 GDP GDP . 
G 5 ACT A 1 604 604 ACT ACT . 
H 2 5GP B 1 600 600 5GP 5GP . 
I 3 ATP B 1 601 601 ATP ATP . 
J 4 GDP B 1 602 602 GDP GDP . 
K 4 GDP B 1 603 603 GDP GDP . 
L 6 HOH A 1 701 25 HOH HOH . 
L 6 HOH A 2 702 36 HOH HOH . 
L 6 HOH A 3 703 16 HOH HOH . 
L 6 HOH A 4 704 20 HOH HOH . 
L 6 HOH A 5 705 17 HOH HOH . 
L 6 HOH A 6 706 23 HOH HOH . 
L 6 HOH A 7 707 7 HOH HOH . 
L 6 HOH A 8 708 1 HOH HOH . 
L 6 HOH A 9 709 12 HOH HOH . 
L 6 HOH A 10 710 2 HOH HOH . 
L 6 HOH A 11 711 24 HOH HOH . 
L 6 HOH A 12 712 21 HOH HOH . 
L 6 HOH A 13 713 37 HOH HOH . 
L 6 HOH A 14 714 43 HOH HOH . 
L 6 HOH A 15 715 46 HOH HOH . 
L 6 HOH A 16 716 39 HOH HOH . 
L 6 HOH A 17 717 41 HOH HOH . 
L 6 HOH A 18 718 19 HOH HOH . 
L 6 HOH A 19 719 22 HOH HOH . 
L 6 HOH A 20 720 47 HOH HOH . 
L 6 HOH A 21 721 49 HOH HOH . 
L 6 HOH A 22 722 53 HOH HOH . 
L 6 HOH A 23 723 40 HOH HOH . 
L 6 HOH A 24 724 52 HOH HOH . 
L 6 HOH A 25 725 51 HOH HOH . 
L 6 HOH A 26 726 45 HOH HOH . 
L 6 HOH A 27 727 44 HOH HOH . 
L 6 HOH A 28 728 48 HOH HOH . 
M 6 HOH B 1 701 8 HOH HOH . 
M 6 HOH B 2 702 13 HOH HOH . 
M 6 HOH B 3 703 27 HOH HOH . 
M 6 HOH B 4 704 15 HOH HOH . 
M 6 HOH B 5 705 3 HOH HOH . 
M 6 HOH B 6 706 6 HOH HOH . 
M 6 HOH B 7 707 11 HOH HOH . 
M 6 HOH B 8 708 31 HOH HOH . 
M 6 HOH B 9 709 30 HOH HOH . 
M 6 HOH B 10 710 29 HOH HOH . 
M 6 HOH B 11 711 5 HOH HOH . 
M 6 HOH B 12 712 14 HOH HOH . 
M 6 HOH B 13 713 26 HOH HOH . 
M 6 HOH B 14 714 28 HOH HOH . 
M 6 HOH B 15 715 9 HOH HOH . 
M 6 HOH B 16 716 32 HOH HOH . 
M 6 HOH B 17 717 10 HOH HOH . 
M 6 HOH B 18 718 34 HOH HOH . 
M 6 HOH B 19 719 33 HOH HOH . 
M 6 HOH B 20 720 54 HOH HOH . 
M 6 HOH B 21 721 35 HOH HOH . 
M 6 HOH B 22 722 50 HOH HOH . 
M 6 HOH B 23 723 42 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 . . . E 4 -54.429 8.191 -2.113 1 68.72 ? PB GDP 602 A 1 
HETATM 2 O O1B GDP . . . E 4 -54.019 8.856 -3.404 1 68.81 ? O1B GDP 602 A 1 
HETATM 3 O O2B GDP . . . E 4 -55.169 6.911 -2.415 1 68.97 ? O2B GDP 602 A 1 
HETATM 4 O O3B GDP . . . E 4 -55.281 9.136 -1.297 1 68.06 ? O3B GDP 602 A 1 
HETATM 5 O O3A GDP . . . E 4 -53.164 7.823 -1.249 1 69.42 ? O3A GDP 602 A 1 
HETATM 6 P PA GDP . . . E 4 -53.323 6.909 0.028 1 69.4 ? PA GDP 602 A 1 
HETATM 7 O O1A GDP . . . E 4 -53.222 5.454 -0.355 1 69 ? O1A GDP 602 A 1 
HETATM 8 O O2A GDP . . . E 4 -54.696 7.183 0.601 1 70.06 ? O2A GDP 602 A 1 
HETATM 9 O O5' GDP . . . E 4 -52.217 7.302 1.09 1 68.73 ? O5' GDP 602 A 1 
HETATM 10 C C5' GDP . . . E 4 -52.202 8.654 1.5 1 68.52 ? C5' GDP 602 A 1 
HETATM 11 C C4' GDP . . . E 4 -51.406 8.815 2.73 1 68.59 ? C4' GDP 602 A 1 
HETATM 12 O O4' GDP . . . E 4 -51.051 10.269 2.896 1 69.1 ? O4' GDP 602 A 1 
HETATM 13 C C3' GDP . . . E 4 -52.191 8.401 3.9 1 68.32 ? C3' GDP 602 A 1 
HETATM 14 O O3' GDP . . . E 4 -51.357 7.637 4.822 1 68.35 ? O3' GDP 602 A 1 
HETATM 15 C C2' GDP . . . E 4 -52.624 9.611 4.558 1 68.78 ? C2' GDP 602 A 1 
HETATM 16 O O2' GDP . . . E 4 -52.696 9.397 5.996 1 68.96 ? O2' GDP 602 A 1 
HETATM 17 C C1' GDP . . . E 4 -51.605 10.625 4.245 1 69.01 ? C1' GDP 602 A 1 
HETATM 18 N N9 GDP . . . E 4 -52.133 11.902 4.204 1 69.21 ? N9 GDP 602 A 1 
HETATM 19 C C8 GDP . . . E 4 -51.732 12.94 4.942 1 69.1 ? C8 GDP 602 A 1 
HETATM 20 N N7 GDP . . . E 4 -52.442 14.006 4.645 1 69.13 ? N7 GDP 602 A 1 
HETATM 21 C C5 GDP . . . E 4 -53.324 13.689 3.7 1 68.9 ? C5 GDP 602 A 1 
HETATM 22 C C6 GDP . . . E 4 -54.36 14.428 2.981 1 67.95 ? C6 GDP 602 A 1 
HETATM 23 O O6 GDP . . . E 4 -54.535 15.601 3.227 1 67.9 ? O6 GDP 602 A 1 
HETATM 24 N N1 GDP . . . E 4 -55.133 13.789 2.022 1 67.69 ? N1 GDP 602 A 1 
HETATM 25 C C2 GDP . . . E 4 -54.919 12.396 1.732 1 68.03 ? C2 GDP 602 A 1 
HETATM 26 N N2 GDP . . . E 4 -55.709 11.744 0.753 1 67.87 ? N2 GDP 602 A 1 
HETATM 27 N N3 GDP . . . E 4 -53.964 11.7 2.392 1 68.77 ? N3 GDP 602 A 1 
HETATM 28 C C4 GDP . . . E 4 -53.141 12.346 3.396 1 69.17 ? C4 GDP 602 A 1 
HETATM 29 H H5' GDP . . . E 4 -51.818 9.206 0.786 1 82.22 ? H5' GDP 602 A 1 
HETATM 30 H "H5''" GDP . . . E 4 -53.121 8.946 1.675 1 82.22 ? "H5''" GDP 602 A 1 
HETATM 31 H H4' GDP . . . E 4 -50.592 8.28 2.671 1 82.31 ? H4' GDP 602 A 1 
HETATM 32 H H3' GDP . . . E 4 -52.961 7.873 3.622 1 81.99 ? H3' GDP 602 A 1 
HETATM 33 H H2' GDP . . . E 4 -53.495 9.89 4.213 1 82.53 ? H2' GDP 602 A 1 
HETATM 34 H HO2' GDP . . . E 4 -53.536 9.226 6.228 1 82.75 ? HO2' GDP 602 A 1 
HETATM 35 H H1' GDP . . . E 4 -50.892 10.588 4.912 1 82.82 ? H1' GDP 602 A 1 
HETATM 36 H H8 GDP . . . E 4 -51.02 12.91 5.608 1 82.92 ? H8 GDP 602 A 1 
HETATM 37 H HN1 GDP . . . E 4 -55.777 14.253 1.575 1 81.22 ? HN1 GDP 602 A 1 
HETATM 38 H HN21 GDP . . . E 4 -55.572 10.856 0.57 1 81.44 ? HN21 GDP 602 A 1 
HETATM 39 H HN22 GDP . . . E 4 -56.356 12.208 0.305 1 81.44 ? HN22 GDP 602 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#