data_3FBE
#
_model_server_result.job_id            027tuDYeBOEN2wKeVhAAbA 
_model_server_result.datetime_utc      '2024-11-13 07:17:55' 
_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          3fbe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":138}' 
#
_entry.id    3FBE 
#
_exptl.entry_id    3FBE 
_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    6 
_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            3FBE 
_cell.length_a            79.243 
_cell.length_b            152.897 
_cell.length_c            183.785 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3FBE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? hexameric 6 author_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,G,H,J,K,N,O,R,T,V 1 1,2 
B,D,F,I,L,M,P,Q,S,U,W 2 1,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 158.486 0 91.8925 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 I N N 
? 3 K N N 
? 3 M N N 
? 3 O N N 
? 3 Q 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 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                     3FBE 
_atom_sites.fract_transf_matrix[1][1]    0.012619 
_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]    0.00654 
_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]    0.005441 
_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 2 MG A 1 160 160 MG MG . 
H 3 GDP A 1 138 1 GDP GDP . 
I 3 GDP B 1 138 1 GDP GDP . 
J 2 MG C 1 162 162 MG MG . 
K 3 GDP C 1 138 1 GDP GDP . 
L 2 MG D 1 163 163 MG MG . 
M 3 GDP D 1 138 1 GDP GDP . 
N 2 MG E 1 164 164 MG MG . 
O 3 GDP E 1 138 1 GDP GDP . 
P 2 MG F 1 165 165 MG MG . 
Q 3 GDP F 1 138 1 GDP GDP . 
R 4 HOH A 1 139 3 HOH HOH . 
R 4 HOH A 2 140 5 HOH HOH . 
R 4 HOH A 3 141 7 HOH HOH . 
R 4 HOH A 4 142 9 HOH HOH . 
R 4 HOH A 5 143 10 HOH HOH . 
R 4 HOH A 6 144 144 HOH HOH . 
R 4 HOH A 7 145 145 HOH HOH . 
R 4 HOH A 8 146 15 HOH HOH . 
R 4 HOH A 9 147 22 HOH HOH . 
R 4 HOH A 10 148 25 HOH HOH . 
R 4 HOH A 11 149 28 HOH HOH . 
R 4 HOH A 12 150 150 HOH HOH . 
R 4 HOH A 13 151 29 HOH HOH . 
R 4 HOH A 14 152 30 HOH HOH . 
R 4 HOH A 15 153 31 HOH HOH . 
R 4 HOH A 16 154 34 HOH HOH . 
R 4 HOH A 17 155 51 HOH HOH . 
R 4 HOH A 18 156 52 HOH HOH . 
R 4 HOH A 19 157 75 HOH HOH . 
R 4 HOH A 20 158 96 HOH HOH . 
R 4 HOH A 21 159 97 HOH HOH . 
R 4 HOH A 22 161 99 HOH HOH . 
R 4 HOH A 23 162 108 HOH HOH . 
R 4 HOH A 24 163 113 HOH HOH . 
R 4 HOH A 25 164 114 HOH HOH . 
R 4 HOH A 26 165 124 HOH HOH . 
R 4 HOH A 27 166 126 HOH HOH . 
R 4 HOH A 28 167 127 HOH HOH . 
R 4 HOH A 29 168 136 HOH HOH . 
R 4 HOH A 30 169 138 HOH HOH . 
S 4 HOH B 1 139 27 HOH HOH . 
S 4 HOH B 2 140 37 HOH HOH . 
S 4 HOH B 3 141 39 HOH HOH . 
S 4 HOH B 4 142 142 HOH HOH . 
S 4 HOH B 5 143 40 HOH HOH . 
S 4 HOH B 6 144 55 HOH HOH . 
S 4 HOH B 7 145 64 HOH HOH . 
S 4 HOH B 8 146 74 HOH HOH . 
S 4 HOH B 9 147 147 HOH HOH . 
S 4 HOH B 10 148 79 HOH HOH . 
S 4 HOH B 11 149 149 HOH HOH . 
S 4 HOH B 12 150 83 HOH HOH . 
S 4 HOH B 13 151 85 HOH HOH . 
S 4 HOH B 14 152 88 HOH HOH . 
S 4 HOH B 15 153 106 HOH HOH . 
S 4 HOH B 16 154 131 HOH HOH . 
S 4 HOH B 17 155 132 HOH HOH . 
T 4 HOH C 1 139 4 HOH HOH . 
T 4 HOH C 2 140 6 HOH HOH . 
T 4 HOH C 3 141 8 HOH HOH . 
T 4 HOH C 4 142 11 HOH HOH . 
T 4 HOH C 5 143 12 HOH HOH . 
T 4 HOH C 6 144 14 HOH HOH . 
T 4 HOH C 7 145 18 HOH HOH . 
T 4 HOH C 8 146 19 HOH HOH . 
T 4 HOH C 9 147 23 HOH HOH . 
T 4 HOH C 10 148 24 HOH HOH . 
T 4 HOH C 11 149 42 HOH HOH . 
T 4 HOH C 12 150 44 HOH HOH . 
T 4 HOH C 13 151 46 HOH HOH . 
T 4 HOH C 14 152 66 HOH HOH . 
T 4 HOH C 15 153 82 HOH HOH . 
T 4 HOH C 16 154 89 HOH HOH . 
T 4 HOH C 17 155 90 HOH HOH . 
T 4 HOH C 18 156 91 HOH HOH . 
T 4 HOH C 19 157 92 HOH HOH . 
T 4 HOH C 20 158 95 HOH HOH . 
T 4 HOH C 21 159 98 HOH HOH . 
T 4 HOH C 22 160 100 HOH HOH . 
T 4 HOH C 23 161 112 HOH HOH . 
T 4 HOH C 24 163 122 HOH HOH . 
T 4 HOH C 25 164 137 HOH HOH . 
U 4 HOH D 1 139 17 HOH HOH . 
U 4 HOH D 2 140 35 HOH HOH . 
U 4 HOH D 3 141 49 HOH HOH . 
U 4 HOH D 4 142 50 HOH HOH . 
U 4 HOH D 5 143 53 HOH HOH . 
U 4 HOH D 6 144 54 HOH HOH . 
U 4 HOH D 7 145 56 HOH HOH . 
U 4 HOH D 8 146 58 HOH HOH . 
U 4 HOH D 9 147 68 HOH HOH . 
U 4 HOH D 10 148 69 HOH HOH . 
U 4 HOH D 11 149 76 HOH HOH . 
U 4 HOH D 12 150 77 HOH HOH . 
U 4 HOH D 13 151 78 HOH HOH . 
U 4 HOH D 14 152 93 HOH HOH . 
U 4 HOH D 15 153 101 HOH HOH . 
U 4 HOH D 16 154 102 HOH HOH . 
U 4 HOH D 17 155 103 HOH HOH . 
U 4 HOH D 18 156 104 HOH HOH . 
U 4 HOH D 19 157 105 HOH HOH . 
U 4 HOH D 20 158 111 HOH HOH . 
U 4 HOH D 21 159 117 HOH HOH . 
U 4 HOH D 22 160 120 HOH HOH . 
U 4 HOH D 23 161 125 HOH HOH . 
U 4 HOH D 24 162 133 HOH HOH . 
U 4 HOH D 25 164 134 HOH HOH . 
V 4 HOH E 1 139 139 HOH HOH . 
V 4 HOH E 2 140 140 HOH HOH . 
V 4 HOH E 3 141 1 HOH HOH . 
V 4 HOH E 4 142 16 HOH HOH . 
V 4 HOH E 5 143 143 HOH HOH . 
V 4 HOH E 6 144 20 HOH HOH . 
V 4 HOH E 7 145 26 HOH HOH . 
V 4 HOH E 8 146 33 HOH HOH . 
V 4 HOH E 9 147 36 HOH HOH . 
V 4 HOH E 10 148 43 HOH HOH . 
V 4 HOH E 11 149 45 HOH HOH . 
V 4 HOH E 12 150 47 HOH HOH . 
V 4 HOH E 13 151 48 HOH HOH . 
V 4 HOH E 14 152 61 HOH HOH . 
V 4 HOH E 15 153 62 HOH HOH . 
V 4 HOH E 16 154 63 HOH HOH . 
V 4 HOH E 17 155 65 HOH HOH . 
V 4 HOH E 18 156 67 HOH HOH . 
V 4 HOH E 19 157 72 HOH HOH . 
V 4 HOH E 20 158 73 HOH HOH . 
V 4 HOH E 21 159 80 HOH HOH . 
V 4 HOH E 22 160 86 HOH HOH . 
V 4 HOH E 23 161 87 HOH HOH . 
V 4 HOH E 24 162 107 HOH HOH . 
V 4 HOH E 25 163 119 HOH HOH . 
V 4 HOH E 26 165 123 HOH HOH . 
V 4 HOH E 27 166 128 HOH HOH . 
V 4 HOH E 28 167 129 HOH HOH . 
W 4 HOH F 1 139 2 HOH HOH . 
W 4 HOH F 2 140 13 HOH HOH . 
W 4 HOH F 3 141 141 HOH HOH . 
W 4 HOH F 4 142 21 HOH HOH . 
W 4 HOH F 5 143 32 HOH HOH . 
W 4 HOH F 6 144 38 HOH HOH . 
W 4 HOH F 7 145 41 HOH HOH . 
W 4 HOH F 8 146 146 HOH HOH . 
W 4 HOH F 9 147 57 HOH HOH . 
W 4 HOH F 10 148 148 HOH HOH . 
W 4 HOH F 11 149 59 HOH HOH . 
W 4 HOH F 12 150 60 HOH HOH . 
W 4 HOH F 13 151 70 HOH HOH . 
W 4 HOH F 14 152 71 HOH HOH . 
W 4 HOH F 15 153 81 HOH HOH . 
W 4 HOH F 16 154 84 HOH HOH . 
W 4 HOH F 17 155 94 HOH HOH . 
W 4 HOH F 18 156 109 HOH HOH . 
W 4 HOH F 19 157 110 HOH HOH . 
W 4 HOH F 20 158 115 HOH HOH . 
W 4 HOH F 21 159 116 HOH HOH . 
W 4 HOH F 22 160 118 HOH HOH . 
W 4 HOH F 23 161 121 HOH HOH . 
W 4 HOH F 24 162 130 HOH HOH . 
W 4 HOH F 25 163 135 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 71.872 33.726 67.275 1 89.94 ? PB GDP 138 D 1 
HETATM 2 O O1B GDP . . . M 3 72.134 32.501 66.441 1 72.92 ? O1B GDP 138 D 1 
HETATM 3 O O2B GDP . . . M 3 73.215 34.231 67.749 1 77.27 ? O2B GDP 138 D 1 
HETATM 4 O O3B GDP . . . M 3 71.183 34.77 66.421 1 74.06 ? O3B GDP 138 D 1 
HETATM 5 O O3A GDP . . . M 3 70.9 33.393 68.527 1 100.36 ? O3A GDP 138 D 1 
HETATM 6 P PA GDP . . . M 3 70.723 31.899 69.126 1 108.84 ? PA GDP 138 D 1 
HETATM 7 O O1A GDP . . . M 3 69.346 31.748 69.74 1 94.68 ? O1A GDP 138 D 1 
HETATM 8 O O2A GDP . . . M 3 71.804 31.618 70.149 1 91.22 ? O2A GDP 138 D 1 
HETATM 9 O O5' GDP . . . M 3 70.863 30.942 67.829 1 81.84 ? O5' GDP 138 D 1 
HETATM 10 C C5' GDP . . . M 3 71.52 29.682 67.948 1 73.39 ? C5' GDP 138 D 1 
HETATM 11 C C4' GDP . . . M 3 72.447 29.352 66.776 1 68.83 ? C4' GDP 138 D 1 
HETATM 12 O O4' GDP . . . M 3 72.477 27.927 66.669 1 72.46 ? O4' GDP 138 D 1 
HETATM 13 C C3' GDP . . . M 3 72.016 29.887 65.412 1 66.04 ? C3' GDP 138 D 1 
HETATM 14 O O3' GDP . . . M 3 72.954 30.845 64.919 1 59.21 ? O3' GDP 138 D 1 
HETATM 15 C C2' GDP . . . M 3 72.016 28.7 64.475 1 63.3 ? C2' GDP 138 D 1 
HETATM 16 O O2' GDP . . . M 3 73.244 28.668 63.739 1 57.46 ? O2' GDP 138 D 1 
HETATM 17 C C1' GDP . . . M 3 71.938 27.515 65.413 1 62.59 ? C1' GDP 138 D 1 
HETATM 18 N N9 GDP . . . M 3 70.506 27.172 65.595 1 71.35 ? N9 GDP 138 D 1 
HETATM 19 C C8 GDP . . . M 3 69.659 27.746 66.478 1 68.43 ? C8 GDP 138 D 1 
HETATM 20 N N7 GDP . . . M 3 68.416 27.21 66.394 1 70 ? N7 GDP 138 D 1 
HETATM 21 C C5 GDP . . . M 3 68.458 26.264 65.428 1 73.46 ? C5 GDP 138 D 1 
HETATM 22 C C6 GDP . . . M 3 67.505 25.302 64.811 1 79.19 ? C6 GDP 138 D 1 
HETATM 23 O O6 GDP . . . M 3 66.313 25.245 65.191 1 81.06 ? O6 GDP 138 D 1 
HETATM 24 N N1 GDP . . . M 3 67.957 24.495 63.832 1 75.68 ? N1 GDP 138 D 1 
HETATM 25 C C2 GDP . . . M 3 69.233 24.525 63.393 1 76.93 ? C2 GDP 138 D 1 
HETATM 26 N N2 GDP . . . M 3 69.605 23.674 62.4 1 74.23 ? N2 GDP 138 D 1 
HETATM 27 N N3 GDP . . . M 3 70.159 25.377 63.912 1 71.76 ? N3 GDP 138 D 1 
HETATM 28 C C4 GDP . . . M 3 69.836 26.248 64.906 1 73.4 ? C4 GDP 138 D 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#