data_5O2S
#
_model_server_result.job_id            '_iFgYE3-1F5KcqzGPvj9vg' 
_model_server_result.datetime_utc      '2024-11-08 10:37:05' 
_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          5o2s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":201}' 
#
_entry.id    5O2S 
#
_exptl.entry_id    5O2S 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    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         120 
_cell.entry_id            5O2S 
_cell.length_a            197.14 
_cell.length_b            197.14 
_cell.length_c            84.61 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5O2S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,Q,R 1 1 
C,D,K,L,S,T 2 1 
E,F,M,N,U,V 3 1 
G,H,O,P,W 4 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 I N N 
? 3 K N N 
? 3 M N N 
? 3 O 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 OG SER 20 A SER 17 1_555 J MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc2 I O2B GDP . A GDP 201 1_555 J MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc3 J MG MG . A MG 202 1_555 Q O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? 
metalc ? metalc4 J MG MG . A MG 202 1_555 Q O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc5 J MG MG . A MG 202 1_555 Q O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc6 J MG MG . A MG 202 1_555 Q O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
metalc ? metalc7 C OG SER 20 C SER 17 1_555 L MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc8 K O3B GDP . C GDP 201 1_555 L MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc9 L MG MG . C MG 202 1_555 S O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc10 L MG MG . C MG 202 1_555 S O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc11 L MG MG . C MG 202 1_555 S O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc12 L MG MG . C MG 202 1_555 S O HOH . C HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc13 E OG SER 20 E SER 17 1_555 N MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc14 M O3B GDP . E GDP 201 1_555 N MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
metalc ? metalc15 N MG MG . E MG 202 1_555 U O HOH . E HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? 
metalc ? metalc16 N MG MG . E MG 202 1_555 U O HOH . E HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc17 N MG MG . E MG 202 1_555 U O HOH . E HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? 
metalc ? metalc18 N MG MG . E MG 202 1_555 U O HOH . E HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc19 G OG SER 20 G SER 17 1_555 P MG MG . G MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc20 O O3B GDP . G GDP 201 1_555 P MG MG . G MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? 
metalc ? metalc21 P MG MG . G MG 202 1_555 W O HOH . G HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc22 P MG MG . G MG 202 1_555 W O HOH . G HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? 
metalc ? metalc23 P MG MG . G MG 202 1_555 W O HOH . G HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc24 P MG MG . G MG 202 1_555 W O HOH . G HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
#
_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                     5O2S 
_atom_sites.fract_transf_matrix[1][1]    0.005073 
_atom_sites.fract_transf_matrix[1][2]    0.002929 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005857 
_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]    0.011819 
_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
I 3 GDP A 1 201 1 GDP GDP . 
J 4 MG A 1 202 1 MG MG . 
K 3 GDP C 1 201 2 GDP GDP . 
L 4 MG C 1 202 2 MG MG . 
M 3 GDP E 1 201 3 GDP GDP . 
N 4 MG E 1 202 3 MG MG . 
O 3 GDP G 1 201 4 GDP GDP . 
P 4 MG G 1 202 4 MG MG . 
Q 5 HOH A 1 301 2 HOH HOH . 
Q 5 HOH A 2 302 3 HOH HOH . 
Q 5 HOH A 3 303 28 HOH HOH . 
Q 5 HOH A 4 304 1 HOH HOH . 
Q 5 HOH A 5 305 4 HOH HOH . 
Q 5 HOH A 6 306 31 HOH HOH . 
Q 5 HOH A 7 307 27 HOH HOH . 
Q 5 HOH A 8 308 17 HOH HOH . 
Q 5 HOH A 9 309 26 HOH HOH . 
Q 5 HOH A 10 310 58 HOH HOH . 
Q 5 HOH A 11 311 25 HOH HOH . 
Q 5 HOH A 12 312 56 HOH HOH . 
Q 5 HOH A 13 313 29 HOH HOH . 
Q 5 HOH A 14 314 20 HOH HOH . 
R 5 HOH B 1 201 19 HOH HOH . 
R 5 HOH B 2 202 22 HOH HOH . 
R 5 HOH B 3 203 39 HOH HOH . 
R 5 HOH B 4 204 36 HOH HOH . 
R 5 HOH B 5 205 37 HOH HOH . 
R 5 HOH B 6 206 54 HOH HOH . 
S 5 HOH C 1 301 6 HOH HOH . 
S 5 HOH C 2 302 8 HOH HOH . 
S 5 HOH C 3 303 5 HOH HOH . 
S 5 HOH C 4 304 7 HOH HOH . 
S 5 HOH C 5 305 30 HOH HOH . 
S 5 HOH C 6 306 49 HOH HOH . 
S 5 HOH C 7 307 57 HOH HOH . 
S 5 HOH C 8 308 51 HOH HOH . 
S 5 HOH C 9 309 40 HOH HOH . 
S 5 HOH C 10 310 41 HOH HOH . 
S 5 HOH C 11 311 59 HOH HOH . 
S 5 HOH C 12 312 47 HOH HOH . 
S 5 HOH C 13 313 38 HOH HOH . 
S 5 HOH C 14 314 23 HOH HOH . 
S 5 HOH C 15 315 46 HOH HOH . 
S 5 HOH C 16 316 35 HOH HOH . 
S 5 HOH C 17 317 34 HOH HOH . 
S 5 HOH C 18 318 50 HOH HOH . 
S 5 HOH C 19 319 18 HOH HOH . 
S 5 HOH C 20 320 33 HOH HOH . 
T 5 HOH D 1 201 60 HOH HOH . 
T 5 HOH D 2 202 48 HOH HOH . 
U 5 HOH E 1 301 9 HOH HOH . 
U 5 HOH E 2 302 10 HOH HOH . 
U 5 HOH E 3 303 11 HOH HOH . 
U 5 HOH E 4 304 12 HOH HOH . 
U 5 HOH E 5 305 44 HOH HOH . 
U 5 HOH E 6 306 32 HOH HOH . 
U 5 HOH E 7 307 43 HOH HOH . 
U 5 HOH E 8 308 61 HOH HOH . 
U 5 HOH E 9 309 21 HOH HOH . 
U 5 HOH E 10 310 52 HOH HOH . 
U 5 HOH E 11 311 45 HOH HOH . 
U 5 HOH E 12 312 53 HOH HOH . 
V 5 HOH F 1 201 55 HOH HOH . 
W 5 HOH G 1 301 14 HOH HOH . 
W 5 HOH G 2 302 13 HOH HOH . 
W 5 HOH G 3 303 16 HOH HOH . 
W 5 HOH G 4 304 15 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 3 66.379 -55.901 -15 1 46.36 ? PB GDP 201 E 1 
HETATM 2 O O1B GDP . . . M 3 65.991 -54.91 -16.088 1 46.56 ? O1B GDP 201 E 1 
HETATM 3 O O2B GDP . . . M 3 67.683 -56.667 -15.075 1 38.64 ? O2B GDP 201 E 1 
HETATM 4 O O3B GDP . . . M 3 66.082 -55.366 -13.626 1 47.63 ? O3B GDP 201 E 1 
HETATM 5 O O3A GDP . . . M 3 65.335 -57.081 -15.31 1 49.25 ? O3A GDP 201 E 1 
HETATM 6 P PA GDP . . . M 3 63.736 -56.945 -15.13 1 52.78 ? PA GDP 201 E 1 
HETATM 7 O O1A GDP . . . M 3 63.176 -55.587 -15.52 1 52.21 ? O1A GDP 201 E 1 
HETATM 8 O O2A GDP . . . M 3 63.453 -57.522 -13.784 1 51.11 ? O2A GDP 201 E 1 
HETATM 9 O O5' GDP . . . M 3 63.248 -58.053 -16.187 1 56.46 ? O5' GDP 201 E 1 
HETATM 10 C C5' GDP . . . M 3 63.032 -57.753 -17.571 1 59.4 ? C5' GDP 201 E 1 
HETATM 11 C C4' GDP . . . M 3 61.93 -58.643 -18.133 1 58.05 ? C4' GDP 201 E 1 
HETATM 12 O O4' GDP . . . M 3 62.391 -59.986 -18.005 1 57.78 ? O4' GDP 201 E 1 
HETATM 13 C C3' GDP . . . M 3 60.627 -58.527 -17.352 1 59.19 ? C3' GDP 201 E 1 
HETATM 14 O O3' GDP . . . M 3 59.479 -58.431 -18.19 1 64.35 ? O3' GDP 201 E 1 
HETATM 15 C C2' GDP . . . M 3 60.557 -59.802 -16.554 1 56.61 ? C2' GDP 201 E 1 
HETATM 16 O O2' GDP . . . M 3 59.262 -60.356 -16.465 1 55.78 ? O2' GDP 201 E 1 
HETATM 17 C C1' GDP . . . M 3 61.415 -60.764 -17.333 1 55.42 ? C1' GDP 201 E 1 
HETATM 18 N N9 GDP . . . M 3 61.982 -61.725 -16.381 1 54.27 ? N9 GDP 201 E 1 
HETATM 19 C C8 GDP . . . M 3 62.731 -61.444 -15.31 1 54.01 ? C8 GDP 201 E 1 
HETATM 20 N N7 GDP . . . M 3 63.051 -62.577 -14.656 1 55.87 ? N7 GDP 201 E 1 
HETATM 21 C C5 GDP . . . M 3 62.509 -63.608 -15.319 1 57.39 ? C5 GDP 201 E 1 
HETATM 22 C C6 GDP . . . M 3 62.457 -65.089 -15.181 1 56.63 ? C6 GDP 201 E 1 
HETATM 23 O O6 GDP . . . M 3 63.02 -65.7 -14.249 1 53.17 ? O6 GDP 201 E 1 
HETATM 24 N N1 GDP . . . M 3 61.776 -65.779 -16.105 1 58.77 ? N1 GDP 201 E 1 
HETATM 25 C C2 GDP . . . M 3 61.138 -65.191 -17.14 1 57.4 ? C2 GDP 201 E 1 
HETATM 26 N N2 GDP . . . M 3 60.459 -65.964 -18.018 1 54.99 ? N2 GDP 201 E 1 
HETATM 27 N N3 GDP . . . M 3 61.142 -63.841 -17.325 1 58.42 ? N3 GDP 201 E 1 
HETATM 28 C C4 GDP . . . M 3 61.797 -63.026 -16.462 1 56.72 ? C4 GDP 201 E 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    56 
_model_server_stats.query_time_ms           646 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#