data_2W6D
#
_model_server_result.job_id            2y09UoqBvFOfbpLppdyxsQ 
_model_server_result.datetime_utc      '2024-12-22 13:01:41' 
_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          2w6d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"NA","auth_seq_id":1706}' 
#
_entry.id    2W6D 
#
_exptl.entry_id    2W6D 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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            2W6D 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2W6D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               software_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,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA 
_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
? 3 D N N 
? 3 NA 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 214 n n 
PB O2B GDP sing 215 n n 
PB O3B GDP sing 216 n n 
PB O3A GDP sing 217 n n 
O2B HOB2 GDP sing 218 n n 
O3B HOB3 GDP sing 219 n n 
O3A PA GDP sing 220 n n 
PA O1A GDP doub 221 n n 
PA O2A GDP sing 222 n n 
PA O5' GDP sing 223 n n 
O2A HOA2 GDP sing 224 n n 
O5' C5' GDP sing 225 n n 
C5' C4' GDP sing 226 n n 
C5' H5' GDP sing 227 n n 
C5' "H5''" GDP sing 228 n n 
C4' O4' GDP sing 229 n n 
C4' C3' GDP sing 230 n n 
C4' H4' GDP sing 231 n n 
O4' C1' GDP sing 232 n n 
C3' O3' GDP sing 233 n n 
C3' C2' GDP sing 234 n n 
C3' H3' GDP sing 235 n n 
O3' HO3' GDP sing 236 n n 
C2' O2' GDP sing 237 n n 
C2' C1' GDP sing 238 n n 
C2' H2' GDP sing 239 n n 
O2' HO2' GDP sing 240 n n 
C1' N9 GDP sing 241 n n 
C1' H1' GDP sing 242 n n 
N9 C8 GDP sing 243 n y 
N9 C4 GDP sing 244 n y 
C8 N7 GDP doub 245 n y 
C8 H8 GDP sing 246 n n 
N7 C5 GDP sing 247 n y 
C5 C6 GDP sing 248 n n 
C5 C4 GDP doub 249 n y 
C6 O6 GDP doub 250 n n 
C6 N1 GDP sing 251 n n 
N1 C2 GDP sing 252 n n 
N1 HN1 GDP sing 253 n n 
C2 N2 GDP sing 254 n n 
C2 N3 GDP doub 255 n n 
N2 HN21 GDP sing 256 n n 
N2 HN22 GDP sing 257 n n 
N3 C4 GDP sing 258 n n 
#
_atom_sites.entry_id                     2W6D 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 CPL A 1 3077 3077 CPL CPL . 
D 3 GDP A 1 1696 1696 GDP GDP . 
E 2 CPL A 1 1697 1697 CPL CPL . 
F 2 CPL A 1 1698 1698 CPL CPL . 
G 2 CPL A 1 1699 1699 CPL CPL . 
H 2 CPL A 1 1700 1700 CPL CPL . 
I 2 CPL A 1 1701 1701 CPL CPL . 
J 2 CPL A 1 1702 1702 CPL CPL . 
K 2 CPL A 1 1703 1703 CPL CPL . 
L 2 CPL A 1 1704 1704 CPL CPL . 
M 2 CPL A 1 1705 1705 CPL CPL . 
N 2 CPL A 1 1706 1706 CPL CPL . 
O 2 CPL A 1 1707 1707 CPL CPL . 
P 2 CPL A 1 1708 1708 CPL CPL . 
Q 2 CPL A 1 1709 1709 CPL CPL . 
R 2 CPL A 1 1710 1710 CPL CPL . 
S 2 CPL A 1 1711 1711 CPL CPL . 
T 2 CPL A 1 1712 1712 CPL CPL . 
U 2 CPL A 1 1713 1713 CPL CPL . 
V 2 CPL A 1 1714 1714 CPL CPL . 
W 2 CPL A 1 1715 1715 CPL CPL . 
X 2 CPL A 1 1716 1716 CPL CPL . 
Y 2 CPL A 1 1717 1717 CPL CPL . 
Z 2 CPL A 1 1718 1718 CPL CPL . 
AA 2 CPL A 1 3094 3094 CPL CPL . 
BA 2 CPL A 1 3097 3097 CPL CPL . 
CA 2 CPL A 1 3181 3181 CPL CPL . 
DA 2 CPL B 1 1696 1696 CPL CPL . 
EA 2 CPL B 1 1697 1697 CPL CPL . 
FA 2 CPL B 1 1698 1698 CPL CPL . 
GA 2 CPL B 1 1699 1699 CPL CPL . 
HA 2 CPL B 1 1700 1700 CPL CPL . 
IA 2 CPL B 1 1701 1701 CPL CPL . 
JA 2 CPL B 1 1702 1702 CPL CPL . 
KA 2 CPL B 1 1703 1703 CPL CPL . 
LA 2 CPL B 1 1704 1704 CPL CPL . 
MA 2 CPL B 1 1705 1705 CPL CPL . 
NA 3 GDP B 1 1706 1706 GDP GDP . 
OA 2 CPL B 1 1707 1707 CPL CPL . 
PA 2 CPL B 1 1708 1708 CPL CPL . 
QA 2 CPL B 1 1709 1709 CPL CPL . 
RA 2 CPL B 1 1710 1710 CPL CPL . 
SA 2 CPL B 1 1711 1711 CPL CPL . 
TA 2 CPL B 1 1712 1712 CPL CPL . 
UA 2 CPL B 1 1713 1713 CPL CPL . 
VA 2 CPL B 1 1714 1714 CPL CPL . 
#
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 . . . NA 3 228.367 -21.326 49.096 1 63.89 ? PB GDP 1706 B 1 
HETATM 2 O O1B GDP . . . NA 3 228.622 -22.672 49.617 1 64.52 ? O1B GDP 1706 B 1 
HETATM 3 O O2B GDP . . . NA 3 227.011 -20.78 49.738 1 70.52 ? O2B GDP 1706 B 1 
HETATM 4 O O3B GDP . . . NA 3 228.245 -21.343 47.486 1 63.84 ? O3B GDP 1706 B 1 
HETATM 5 O O3A GDP . . . NA 3 229.503 -20.304 49.505 1 61.19 ? O3A GDP 1706 B 1 
HETATM 6 P PA GDP . . . NA 3 230.974 -20.694 48.945 1 57.42 ? PA GDP 1706 B 1 
HETATM 7 O O1A GDP . . . NA 3 231.538 -21.955 49.493 1 39.12 ? O1A GDP 1706 B 1 
HETATM 8 O O2A GDP . . . NA 3 230.944 -20.784 47.343 1 61.33 ? O2A GDP 1706 B 1 
HETATM 9 O O5' GDP . . . NA 3 231.848 -19.451 49.44 1 57.9 ? O5' GDP 1706 B 1 
HETATM 10 C C5' GDP . . . NA 3 233.154 -19.653 49.018 1 63.66 ? C5' GDP 1706 B 1 
HETATM 11 C C4' GDP . . . NA 3 233.954 -18.453 49.438 1 58.81 ? C4' GDP 1706 B 1 
HETATM 12 O O4' GDP . . . NA 3 233.857 -18.285 50.856 1 52.01 ? O4' GDP 1706 B 1 
HETATM 13 C C3' GDP . . . NA 3 235.392 -18.696 49.013 1 65.25 ? C3' GDP 1706 B 1 
HETATM 14 O O3' GDP . . . NA 3 235.854 -17.678 48.102 1 70.19 ? O3' GDP 1706 B 1 
HETATM 15 C C2' GDP . . . NA 3 236.189 -18.738 50.307 1 65.66 ? C2' GDP 1706 B 1 
HETATM 16 O O2' GDP . . . NA 3 237.235 -17.757 50.288 1 78.2 ? O2' GDP 1706 B 1 
HETATM 17 C C1' GDP . . . NA 3 235.161 -18.465 51.43 1 61.04 ? C1' GDP 1706 B 1 
HETATM 18 N N9 GDP . . . NA 3 235.144 -19.537 52.426 1 55.92 ? N9 GDP 1706 B 1 
HETATM 19 C C8 GDP . . . NA 3 234.404 -20.691 52.415 1 59.41 ? C8 GDP 1706 B 1 
HETATM 20 N N7 GDP . . . NA 3 234.664 -21.394 53.481 1 57.68 ? N7 GDP 1706 B 1 
HETATM 21 C C5 GDP . . . NA 3 235.583 -20.735 54.228 1 54.75 ? C5 GDP 1706 B 1 
HETATM 22 C C6 GDP . . . NA 3 236.25 -20.988 55.471 1 53.51 ? C6 GDP 1706 B 1 
HETATM 23 O O6 GDP . . . NA 3 236.027 -22.006 56.111 1 47.39 ? O6 GDP 1706 B 1 
HETATM 24 N N1 GDP . . . NA 3 237.157 -20.054 55.924 1 55.16 ? N1 GDP 1706 B 1 
HETATM 25 C C2 GDP . . . NA 3 237.413 -18.902 55.199 1 51.92 ? C2 GDP 1706 B 1 
HETATM 26 N N2 GDP . . . NA 3 238.318 -17.995 55.664 1 51.16 ? N2 GDP 1706 B 1 
HETATM 27 N N3 GDP . . . NA 3 236.797 -18.667 54.064 1 49.43 ? N3 GDP 1706 B 1 
HETATM 28 C C4 GDP . . . NA 3 235.896 -19.539 53.549 1 52.95 ? C4 GDP 1706 B 1 
#
_model_server_stats.io_time_ms              94 
_model_server_stats.parse_time_ms           180 
_model_server_stats.create_model_time_ms    165 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#