data_8CLG
#
_model_server_result.job_id            tGnx7zgdqBm9GWT51Ar3Jg 
_model_server_result.datetime_utc      '2024-11-05 08:36:54' 
_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          8clg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":505}' 
#
_entry.id    8CLG 
#
_exptl.entry_id    8CLG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          10 
_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            8CLG 
_cell.length_a            106.76 
_cell.length_b            160.76 
_cell.length_c            180.96 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8CLG 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_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 
_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
? 10 N N N 
? 10 T 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? 
metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc7 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? 
metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
metalc ? metalc9 H MG MG . A MG 502 1_555 W O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc10 H MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc11 B OE1 GLN 11 B GLN 11 1_555 O MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc12 B OE2 GLU 111 B GLU 113 1_555 K CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc13 K CA CA . B CA 502 1_555 Y O HOH . C HOH 618 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc14 N O1A GDP . B GDP 505 1_555 O MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc15 O MG MG . B MG 506 1_555 X O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc16 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? 
metalc ? metalc17 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc18 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? 
metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? 
metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc22 C OD2 ASP 69 C ASP 69 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? 
metalc ? metalc23 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
metalc ? metalc24 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc25 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc26 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc27 D OE1 GLN 11 D GLN 11 1_555 U MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? 
metalc ? metalc28 T O1A GDP . D GDP 502 1_555 U MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
#
_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 209 n n 
PB O2B GDP sing 210 n n 
PB O3B GDP sing 211 n n 
PB O3A GDP sing 212 n n 
O2B HOB2 GDP sing 213 n n 
O3B HOB3 GDP sing 214 n n 
O3A PA GDP sing 215 n n 
PA O1A GDP doub 216 n n 
PA O2A GDP sing 217 n n 
PA O5' GDP sing 218 n n 
O2A HOA2 GDP sing 219 n n 
O5' C5' GDP sing 220 n n 
C5' C4' GDP sing 221 n n 
C5' H5' GDP sing 222 n n 
C5' "H5''" GDP sing 223 n n 
C4' O4' GDP sing 224 n n 
C4' C3' GDP sing 225 n n 
C4' H4' GDP sing 226 n n 
O4' C1' GDP sing 227 n n 
C3' O3' GDP sing 228 n n 
C3' C2' GDP sing 229 n n 
C3' H3' GDP sing 230 n n 
O3' HO3' GDP sing 231 n n 
C2' O2' GDP sing 232 n n 
C2' C1' GDP sing 233 n n 
C2' H2' GDP sing 234 n n 
O2' HO2' GDP sing 235 n n 
C1' N9 GDP sing 236 n n 
C1' H1' GDP sing 237 n n 
N9 C8 GDP sing 238 n y 
N9 C4 GDP sing 239 n y 
C8 N7 GDP doub 240 n y 
C8 H8 GDP sing 241 n n 
N7 C5 GDP sing 242 n y 
C5 C6 GDP sing 243 n n 
C5 C4 GDP doub 244 n y 
C6 O6 GDP doub 245 n n 
C6 N1 GDP sing 246 n n 
N1 C2 GDP sing 247 n n 
N1 HN1 GDP sing 248 n n 
C2 N2 GDP sing 249 n n 
C2 N3 GDP doub 250 n n 
N2 HN21 GDP sing 251 n n 
N2 HN22 GDP sing 252 n n 
N3 C4 GDP sing 253 n n 
#
_atom_sites.entry_id                     8CLG 
_atom_sites.fract_transf_matrix[1][1]    0.009367 
_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]    0.00622 
_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]    0.005526 
_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 7 CA B 1 501 504 CA CA . 
K 7 CA B 1 502 505 CA CA . 
L 8 EP B 1 503 506 EP EPA . 
M 9 LOC B 1 504 507 LOC COL . 
N 10 GDP B 1 505 508 GDP GDP . 
O 6 MG B 1 506 509 MG MG . 
P 5 GTP C 1 501 510 GTP GTP . 
Q 6 MG C 1 502 511 MG MG . 
R 7 CA C 1 503 516 CA CA . 
S 8 EP D 1 501 512 EP EPA . 
T 10 GDP D 1 502 513 GDP GDP . 
U 6 MG D 1 503 514 MG MG . 
V 11 ACP F 1 401 515 ACP ACP . 
W 12 HOH A 1 601 6 HOH HOH . 
W 12 HOH A 2 602 10 HOH HOH . 
W 12 HOH A 3 603 23 HOH HOH . 
W 12 HOH A 4 604 66 HOH HOH . 
W 12 HOH A 5 605 50 HOH HOH . 
W 12 HOH A 6 606 30 HOH HOH . 
W 12 HOH A 7 607 4 HOH HOH . 
W 12 HOH A 8 608 47 HOH HOH . 
X 12 HOH B 1 601 36 HOH HOH . 
X 12 HOH B 2 602 13 HOH HOH . 
X 12 HOH B 3 603 22 HOH HOH . 
X 12 HOH B 4 604 48 HOH HOH . 
X 12 HOH B 5 605 14 HOH HOH . 
X 12 HOH B 6 606 69 HOH HOH . 
X 12 HOH B 7 607 44 HOH HOH . 
X 12 HOH B 8 608 37 HOH HOH . 
X 12 HOH B 9 609 51 HOH HOH . 
Y 12 HOH C 1 601 61 HOH HOH . 
Y 12 HOH C 2 602 2 HOH HOH . 
Y 12 HOH C 3 603 3 HOH HOH . 
Y 12 HOH C 4 604 24 HOH HOH . 
Y 12 HOH C 5 605 32 HOH HOH . 
Y 12 HOH C 6 606 64 HOH HOH . 
Y 12 HOH C 7 607 60 HOH HOH . 
Y 12 HOH C 8 608 54 HOH HOH . 
Y 12 HOH C 9 609 49 HOH HOH . 
Y 12 HOH C 10 610 46 HOH HOH . 
Y 12 HOH C 11 611 73 HOH HOH . 
Y 12 HOH C 12 612 41 HOH HOH . 
Y 12 HOH C 13 613 65 HOH HOH . 
Y 12 HOH C 14 614 25 HOH HOH . 
Y 12 HOH C 15 615 16 HOH HOH . 
Y 12 HOH C 16 616 38 HOH HOH . 
Y 12 HOH C 17 617 12 HOH HOH . 
Y 12 HOH C 18 618 19 HOH HOH . 
Y 12 HOH C 19 619 45 HOH HOH . 
Y 12 HOH C 20 620 21 HOH HOH . 
Y 12 HOH C 21 621 43 HOH HOH . 
Z 12 HOH D 1 601 71 HOH HOH . 
Z 12 HOH D 2 602 39 HOH HOH . 
Z 12 HOH D 3 603 79 HOH HOH . 
Z 12 HOH D 4 604 26 HOH HOH . 
AA 12 HOH E 1 201 72 HOH HOH . 
BA 12 HOH F 1 501 40 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 . . . N 10 19.239 51.039 15.718 1 44.14 ? PB GDP 505 B 1 
HETATM 2 O O1B GDP . . . N 10 18.756 51.965 14.624 1 33.05 ? O1B GDP 505 B 1 
HETATM 3 O O2B GDP . . . N 10 20.293 50.072 15.22 1 35.26 ? O2B GDP 505 B 1 
HETATM 4 O O3B GDP . . . N 10 19.913 51.813 16.826 1 42.12 ? O3B GDP 505 B 1 
HETATM 5 O O3A GDP . . . N 10 18.019 50.134 16.265 1 33.49 ? O3A GDP 505 B 1 
HETATM 6 P PA GDP . . . N 10 16.562 50.61 16.778 1 39.73 ? PA GDP 505 B 1 
HETATM 7 O O1A GDP . . . N 10 15.525 50.411 15.67 1 54.02 ? O1A GDP 505 B 1 
HETATM 8 O O2A GDP . . . N 10 16.574 52.039 17.288 1 40.4 ? O2A GDP 505 B 1 
HETATM 9 O O5' GDP . . . N 10 16.343 49.581 18.007 1 34.64 ? O5' GDP 505 B 1 
HETATM 10 C C5' GDP . . . N 10 15.332 48.585 18.101 1 31.97 ? C5' GDP 505 B 1 
HETATM 11 C C4' GDP . . . N 10 14.744 48.682 19.497 1 40.87 ? C4' GDP 505 B 1 
HETATM 12 O O4' GDP . . . N 10 14.351 50.042 19.629 1 40.45 ? O4' GDP 505 B 1 
HETATM 13 C C3' GDP . . . N 10 13.487 47.844 19.651 1 37.35 ? C3' GDP 505 B 1 
HETATM 14 O O3' GDP . . . N 10 13.406 47.317 20.983 1 41.1 ? O3' GDP 505 B 1 
HETATM 15 C C2' GDP . . . N 10 12.348 48.806 19.361 1 40.75 ? C2' GDP 505 B 1 
HETATM 16 O O2' GDP . . . N 10 11.169 48.519 20.116 1 51.09 ? O2' GDP 505 B 1 
HETATM 17 C C1' GDP . . . N 10 12.944 50.114 19.821 1 42.23 ? C1' GDP 505 B 1 
HETATM 18 N N9 GDP . . . N 10 12.502 51.265 19.035 1 37.89 ? N9 GDP 505 B 1 
HETATM 19 C C8 GDP . . . N 10 12.811 51.549 17.768 1 37.85 ? C8 GDP 505 B 1 
HETATM 20 N N7 GDP . . . N 10 12.232 52.727 17.408 1 43.7 ? N7 GDP 505 B 1 
HETATM 21 C C5 GDP . . . N 10 11.567 53.208 18.475 1 40.7 ? C5 GDP 505 B 1 
HETATM 22 C C6 GDP . . . N 10 10.747 54.395 18.79 1 39.07 ? C6 GDP 505 B 1 
HETATM 23 O O6 GDP . . . N 10 10.543 55.265 17.912 1 43.01 ? O6 GDP 505 B 1 
HETATM 24 N N1 GDP . . . N 10 10.231 54.493 20.03 1 38.1 ? N1 GDP 505 B 1 
HETATM 25 C C2 GDP . . . N 10 10.455 53.549 20.974 1 43.31 ? C2 GDP 505 B 1 
HETATM 26 N N2 GDP . . . N 10 9.926 53.681 22.207 1 39.95 ? N2 GDP 505 B 1 
HETATM 27 N N3 GDP . . . N 10 11.186 52.436 20.751 1 36.34 ? N3 GDP 505 B 1 
HETATM 28 C C4 GDP . . . N 10 11.75 52.226 19.542 1 38.94 ? C4 GDP 505 B 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    52 
_model_server_stats.query_time_ms           581 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#