data_5Z4P
#
_model_server_result.job_id            bvmOVQoTLHrGtE6afNy0NQ 
_model_server_result.datetime_utc      '2024-12-22 06:29:04' 
_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          5z4p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":501}' 
#
_entry.id    5Z4P 
#
_exptl.entry_id    5Z4P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          9 
_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            5Z4P 
_cell.length_a            103.832 
_cell.length_b            154.843 
_cell.length_c            181.024 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Z4P 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,FA,GA,HA,IA,JA,KA,LA,MA 
_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
? 9 M N N 
? 9 DA 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 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? 
metalc ? metalc8 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc11 B OE2 GLU 108 B GLU 110 1_555 P CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? 
metalc ? metalc12 B OE1 GLU 111 B GLU 113 1_555 P CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? 
metalc ? metalc13 B OE1 GLU 111 B GLU 113 1_555 Z CA CA . C CA 508 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? 
metalc ? metalc14 B OD2 ASP 177 B ASP 179 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc15 M O2A GDP . B GDP 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc16 N MG MG . B MG 502 1_555 JA O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc17 C OE1 GLU 71 C GLU 71 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? 
metalc ? metalc18 U O3G GTP . C GTP 503 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc19 U O2B GTP . C GTP 503 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc20 V MG MG . C MG 504 1_555 KA O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? 
metalc ? metalc21 DA O2B GDP . D GDP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
#
_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 186 n n 
PB O2B GDP sing 187 n n 
PB O3B GDP sing 188 n n 
PB O3A GDP sing 189 n n 
O2B HOB2 GDP sing 190 n n 
O3B HOB3 GDP sing 191 n n 
O3A PA GDP sing 192 n n 
PA O1A GDP doub 193 n n 
PA O2A GDP sing 194 n n 
PA O5' GDP sing 195 n n 
O2A HOA2 GDP sing 196 n n 
O5' C5' GDP sing 197 n n 
C5' C4' GDP sing 198 n n 
C5' H5' GDP sing 199 n n 
C5' "H5''" GDP sing 200 n n 
C4' O4' GDP sing 201 n n 
C4' C3' GDP sing 202 n n 
C4' H4' GDP sing 203 n n 
O4' C1' GDP sing 204 n n 
C3' O3' GDP sing 205 n n 
C3' C2' GDP sing 206 n n 
C3' H3' GDP sing 207 n n 
O3' HO3' GDP sing 208 n n 
C2' O2' GDP sing 209 n n 
C2' C1' GDP sing 210 n n 
C2' H2' GDP sing 211 n n 
O2' HO2' GDP sing 212 n n 
C1' N9 GDP sing 213 n n 
C1' H1' GDP sing 214 n n 
N9 C8 GDP sing 215 n y 
N9 C4 GDP sing 216 n y 
C8 N7 GDP doub 217 n y 
C8 H8 GDP sing 218 n n 
N7 C5 GDP sing 219 n y 
C5 C6 GDP sing 220 n n 
C5 C4 GDP doub 221 n y 
C6 O6 GDP doub 222 n n 
C6 N1 GDP sing 223 n n 
N1 C2 GDP sing 224 n n 
N1 HN1 GDP sing 225 n n 
C2 N2 GDP sing 226 n n 
C2 N3 GDP doub 227 n n 
N2 HN21 GDP sing 228 n n 
N2 HN22 GDP sing 229 n n 
N3 C4 GDP sing 230 n n 
#
_atom_sites.entry_id                     5Z4P 
_atom_sites.fract_transf_matrix[1][1]    0.009631 
_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]    0.006458 
_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]    0.005524 
_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 GOL A 1 503 504 GOL GOL . 
J 7 GOL A 1 504 505 GOL GOL . 
K 8 CA A 1 505 506 CA CA . 
L 7 GOL A 1 506 201 GOL GOL . 
M 9 GDP B 1 501 501 GDP GDP . 
N 6 MG B 1 502 502 MG MG . 
O 7 GOL B 1 503 506 GOL GOL . 
P 8 CA B 1 504 508 CA CA . 
Q 10 MES B 1 505 509 MES MES . 
R 11 97O B 1 506 999 97O UNK . 
S 7 GOL C 1 501 504 GOL GOL . 
T 7 GOL C 1 502 505 GOL GOL . 
U 5 GTP C 1 503 501 GTP GTP . 
V 6 MG C 1 504 502 MG MG . 
W 7 GOL C 1 505 503 GOL GOL . 
X 7 GOL C 1 506 504 GOL GOL . 
Y 7 GOL C 1 507 505 GOL GOL . 
Z 8 CA C 1 508 508 CA CA . 
AA 12 IMD C 1 509 509 IMD IMD . 
BA 12 IMD C 1 510 510 IMD IMD . 
CA 12 IMD C 1 511 511 IMD IMD . 
DA 9 GDP D 1 501 501 GDP GDP . 
EA 6 MG D 1 502 502 MG MG . 
FA 7 GOL D 1 503 504 GOL GOL . 
GA 7 GOL D 1 504 505 GOL GOL . 
HA 13 ACP F 1 401 402 ACP ACP . 
IA 14 HOH A 1 601 32 HOH HOH . 
IA 14 HOH A 2 602 46 HOH HOH . 
IA 14 HOH A 3 603 34 HOH HOH . 
IA 14 HOH A 4 604 28 HOH HOH . 
IA 14 HOH A 5 605 16 HOH HOH . 
IA 14 HOH A 6 606 30 HOH HOH . 
IA 14 HOH A 7 607 36 HOH HOH . 
IA 14 HOH A 8 608 31 HOH HOH . 
IA 14 HOH A 9 609 10 HOH HOH . 
IA 14 HOH A 10 610 6 HOH HOH . 
IA 14 HOH A 11 611 21 HOH HOH . 
JA 14 HOH B 1 601 17 HOH HOH . 
JA 14 HOH B 2 602 37 HOH HOH . 
JA 14 HOH B 3 603 41 HOH HOH . 
JA 14 HOH B 4 604 40 HOH HOH . 
JA 14 HOH B 5 605 19 HOH HOH . 
JA 14 HOH B 6 606 38 HOH HOH . 
JA 14 HOH B 7 607 42 HOH HOH . 
JA 14 HOH B 8 608 39 HOH HOH . 
JA 14 HOH B 9 609 3 HOH HOH . 
JA 14 HOH B 10 610 7 HOH HOH . 
JA 14 HOH B 11 611 20 HOH HOH . 
JA 14 HOH B 12 612 18 HOH HOH . 
JA 14 HOH B 13 613 44 HOH HOH . 
KA 14 HOH C 1 601 8 HOH HOH . 
KA 14 HOH C 2 602 49 HOH HOH . 
KA 14 HOH C 3 603 14 HOH HOH . 
KA 14 HOH C 4 604 50 HOH HOH . 
KA 14 HOH C 5 605 11 HOH HOH . 
KA 14 HOH C 6 606 45 HOH HOH . 
KA 14 HOH C 7 607 48 HOH HOH . 
KA 14 HOH C 8 608 47 HOH HOH . 
KA 14 HOH C 9 609 4 HOH HOH . 
KA 14 HOH C 10 610 51 HOH HOH . 
KA 14 HOH C 11 611 15 HOH HOH . 
KA 14 HOH C 12 612 1 HOH HOH . 
KA 14 HOH C 13 613 2 HOH HOH . 
KA 14 HOH C 14 614 9 HOH HOH . 
KA 14 HOH C 15 615 5 HOH HOH . 
KA 14 HOH C 16 616 12 HOH HOH . 
KA 14 HOH C 17 617 43 HOH HOH . 
LA 14 HOH D 1 601 52 HOH HOH . 
LA 14 HOH D 2 602 23 HOH HOH . 
LA 14 HOH D 3 603 22 HOH HOH . 
LA 14 HOH D 4 604 25 HOH HOH . 
MA 14 HOH F 1 501 13 HOH HOH . 
MA 14 HOH F 2 502 26 HOH HOH . 
MA 14 HOH F 3 503 27 HOH HOH . 
MA 14 HOH F 4 504 35 HOH HOH . 
MA 14 HOH F 5 505 33 HOH HOH . 
MA 14 HOH F 6 506 24 HOH HOH . 
MA 14 HOH F 7 507 29 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 . . . M 9 18.353 -48.527 -15.9 1 42.97 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . M 9 18.877 -49.266 -17.114 1 40.99 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . M 9 18.037 -49.523 -14.823 1 49.65 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . M 9 19.39 -47.565 -15.358 1 46.64 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . M 9 17.057 -47.649 -16.245 1 47.17 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . M 9 15.706 -48.102 -17.034 1 43.11 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . M 9 15.726 -49.512 -17.593 1 38.41 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . M 9 14.548 -47.812 -16.094 1 48.89 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . M 9 15.716 -46.992 -18.179 1 38.9 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . M 9 14.652 -46.073 -18.336 1 45.54 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . M 9 14.04 -46.241 -19.722 1 45.47 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . M 9 13.523 -47.564 -19.85 1 43.54 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . M 9 12.855 -45.322 -19.838 1 45.35 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . M 9 12.713 -44.937 -21.197 1 49.34 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . M 9 11.665 -46.172 -19.49 1 49.6 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . M 9 10.589 -45.761 -20.327 1 58.04 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . M 9 12.105 -47.527 -19.968 1 47.82 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . M 9 11.633 -48.692 -19.214 1 46.5 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . M 9 11.928 -49.001 -17.947 1 45.95 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . M 9 11.373 -50.194 -17.621 1 50.18 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . M 9 10.732 -50.665 -18.712 1 47.82 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . M 9 9.948 -51.867 -19.063 1 48.8 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . M 9 9.738 -52.769 -18.227 1 48.92 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . M 9 9.46 -51.964 -20.299 1 50.08 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . M 9 9.672 -51.025 -21.226 1 51.12 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . M 9 9.137 -51.219 -22.455 1 50.76 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . M 9 10.382 -49.893 -20.976 1 50.93 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . M 9 10.924 -49.674 -19.761 1 47.33 ? C4 GDP 501 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#