data_6O5N
#
_model_server_result.job_id            ZF4sfKTGlRnHIVky2YXLdg 
_model_server_result.datetime_utc      '2025-01-10 19:00:26' 
_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          6o5n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    6O5N 
#
_exptl.entry_id    6O5N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          8 
_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            6O5N 
_cell.length_a            105.301 
_cell.length_b            157.764 
_cell.length_c            182.084 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6O5N 
_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 
_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
? 8 J N N 
? 8 R 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? 
metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc8 A OE2 GLU 71 A GLU 71 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? 
metalc ? metalc9 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc10 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc11 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc12 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
metalc ? metalc13 J O2A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc14 K MG MG . B MG 502 1_555 U O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? 
metalc ? metalc17 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc19 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? 
metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc22 C OE1 GLU 71 C GLU 71 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc23 O O3G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc24 O O2B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
#
_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                     6O5N 
_atom_sites.fract_transf_matrix[1][1]    0.009497 
_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]    0.006339 
_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]    0.005492 
_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 1 CA CA . 
J 8 GDP B 1 501 501 GDP GDP . 
K 6 MG B 1 502 502 MG MG . 
L 9 MES B 1 503 1 MES MES . 
M 9 MES B 1 504 2 MES MES . 
N 10 QW9 B 1 505 1 QW9 QW9 . 
O 5 GTP C 1 501 501 GTP GTP . 
P 6 MG C 1 502 502 MG MG . 
Q 7 CA C 1 503 2 CA CA . 
R 8 GDP D 1 501 1 GDP GDP . 
S 10 QW9 D 1 502 2 QW9 QW9 . 
T 11 HOH A 1 601 37 HOH HOH . 
T 11 HOH A 2 602 4 HOH HOH . 
T 11 HOH A 3 603 3 HOH HOH . 
T 11 HOH A 4 604 7 HOH HOH . 
T 11 HOH A 5 605 9 HOH HOH . 
T 11 HOH A 6 606 27 HOH HOH . 
T 11 HOH A 7 607 6 HOH HOH . 
T 11 HOH A 8 608 5 HOH HOH . 
T 11 HOH A 9 609 12 HOH HOH . 
T 11 HOH A 10 610 10 HOH HOH . 
T 11 HOH A 11 611 30 HOH HOH . 
T 11 HOH A 12 612 42 HOH HOH . 
T 11 HOH A 13 613 8 HOH HOH . 
T 11 HOH A 14 614 11 HOH HOH . 
U 11 HOH B 1 601 13 HOH HOH . 
U 11 HOH B 2 602 2 HOH HOH . 
U 11 HOH B 3 603 14 HOH HOH . 
U 11 HOH B 4 604 17 HOH HOH . 
U 11 HOH B 5 605 34 HOH HOH . 
U 11 HOH B 6 606 15 HOH HOH . 
U 11 HOH B 7 607 16 HOH HOH . 
V 11 HOH C 1 601 20 HOH HOH . 
V 11 HOH C 2 602 41 HOH HOH . 
V 11 HOH C 3 603 24 HOH HOH . 
V 11 HOH C 4 604 23 HOH HOH . 
V 11 HOH C 5 605 26 HOH HOH . 
V 11 HOH C 6 606 19 HOH HOH . 
V 11 HOH C 7 607 18 HOH HOH . 
V 11 HOH C 8 608 25 HOH HOH . 
V 11 HOH C 9 609 38 HOH HOH . 
V 11 HOH C 10 610 28 HOH HOH . 
V 11 HOH C 11 611 21 HOH HOH . 
V 11 HOH C 12 612 31 HOH HOH . 
V 11 HOH C 13 613 22 HOH HOH . 
W 11 HOH D 1 601 1 HOH HOH . 
W 11 HOH D 2 602 33 HOH HOH . 
W 11 HOH D 3 603 43 HOH HOH . 
X 11 HOH E 1 201 40 HOH HOH . 
Y 11 HOH F 1 401 35 HOH HOH . 
Y 11 HOH F 2 402 36 HOH HOH . 
Y 11 HOH F 3 403 39 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 . . . J 8 18.555 -49.549 -15.974 1 32.02 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . J 8 18.921 -50.396 -17.166 1 31.2 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . J 8 18.179 -50.423 -14.806 1 29.1 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . J 8 19.745 -48.711 -15.578 1 35.54 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . J 8 17.335 -48.56 -16.324 1 34.55 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . J 8 15.946 -49.063 -16.97 1 31.64 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . J 8 16.053 -50.475 -17.503 1 26.75 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . J 8 14.829 -48.964 -15.956 1 31.76 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . J 8 15.706 -48.011 -18.166 1 21 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . J 8 14.508 -47.25 -18.231 1 22.19 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . J 8 14.012 -47.212 -19.667 1 24.94 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . J 8 13.624 -48.538 -20.019 1 26.65 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . J 8 12.772 -46.35 -19.789 1 25.99 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . J 8 12.744 -45.714 -21.071 1 27.17 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . J 8 11.621 -47.325 -19.688 1 26.98 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . J 8 10.539 -46.902 -20.519 1 27.99 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . J 8 12.207 -48.63 -20.192 1 27.32 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . J 8 11.709 -49.801 -19.432 1 30 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . J 8 11.981 -50.095 -18.145 1 32.6 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . J 8 11.381 -51.256 -17.77 1 34.55 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . J 8 10.714 -51.726 -18.842 1 32.23 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . J 8 9.871 -52.903 -19.146 1 30.46 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . J 8 9.631 -53.765 -18.276 1 28.54 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . J 8 9.371 -53.016 -20.382 1 32.02 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . J 8 9.609 -52.105 -21.344 1 31.91 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . J 8 9.065 -52.29 -22.571 1 29.27 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . J 8 10.372 -51.002 -21.139 1 32.7 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . J 8 10.936 -50.765 -19.932 1 31.71 ? C4 GDP 501 B 1 
#
_model_server_stats.io_time_ms              40 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           28 
#