data_6Q94
#
_model_server_result.job_id            TO3CslZ32AVSMU6HXgVnyA 
_model_server_result.datetime_utc      '2024-10-11 06:25:02' 
_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          6q94 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":402}' 
#
_entry.id    6Q94 
#
_exptl.entry_id    6Q94 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              605.341 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_entity.pdbx_number_of_molecules    8 
_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            6Q94 
_cell.length_a            101.62 
_cell.length_b            231.06 
_cell.length_c            383.89 
_cell.Z_PDB               64 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Q94 
_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
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
PISA tetrameric 4 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L,CA 1 1,3 
C,D,E,F,M,N,O,P,Q,R,S,T,U,V,DA,EA 2 1 
G,H,W,X,Y,Z,AA,BA,FA 3 1,2 
#
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' 3_855 -x+3,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 304.86 0 191.945 
3 'crystal symmetry operation' 4_575 x,-y+2,-z 1 0 0 0 -1 0 0 0 -1 0 462.12 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 T N N 
? 3 U N N 
? 3 X N N 
? 3 AA N N 
#
_chem_comp.formula           'C16 H25 N5 O16 P2' 
_chem_comp.formula_weight    605.341 
_chem_comp.id                GDD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_chem_comp.type              non-polymer 
_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
N2 C2 GDD sing 92 n n 
N2 H2N1 GDD sing 93 n n 
N2 H2N2 GDD sing 94 n n 
C2 N1 GDD sing 95 n n 
C2 N3 GDD doub 96 n n 
N1 C6 GDD sing 97 n n 
N1 H1 GDD sing 98 n n 
N3 C4 GDD sing 99 n n 
C4 C5 GDD doub 100 n y 
C4 N9 GDD sing 101 n y 
C5 C6 GDD sing 102 n n 
C5 N7 GDD sing 103 n y 
C6 O6 GDD doub 104 n n 
N7 C8 GDD doub 105 n y 
C8 N9 GDD sing 106 n y 
C8 H8 GDD sing 107 n n 
N9 C1' GDD sing 108 n n 
C1' C2' GDD sing 109 n n 
C1' O4' GDD sing 110 n n 
C1' H1' GDD sing 111 n n 
C2' O2' GDD sing 112 n n 
C2' C3' GDD sing 113 n n 
C2' H2' GDD sing 114 n n 
O2' HA GDD sing 115 n n 
C3' O3' GDD sing 116 n n 
C3' C4' GDD sing 117 n n 
C3' H3' GDD sing 118 n n 
O3' HB GDD sing 119 n n 
C4' O4' GDD sing 120 n n 
C4' C5' GDD sing 121 n n 
C4' H4' GDD sing 122 n n 
C5' O5' GDD sing 123 n n 
C5' "H5'1" GDD sing 124 n n 
C5' "H5'2" GDD sing 125 n n 
O5' PA GDD sing 126 n n 
PA O1A GDD doub 127 n n 
PA O2A GDD sing 128 n n 
PA O3A GDD sing 129 n n 
O2A HO2A GDD sing 130 n n 
O3A PB GDD sing 131 n n 
PB O2B GDD sing 132 n n 
PB O3B GDD doub 133 n n 
PB O1B GDD sing 134 n n 
O2B HO2B GDD sing 135 n n 
O1B C11 GDD sing 136 n n 
C11 O51 GDD sing 137 n n 
C11 C21 GDD sing 138 n n 
C11 H11 GDD sing 139 n n 
O51 C51 GDD sing 140 n n 
C51 C61 GDD sing 141 n n 
C51 C41 GDD sing 142 n n 
C51 H51 GDD sing 143 n n 
C61 O6A GDD sing 144 n n 
C61 H611 GDD sing 145 n n 
C61 H612 GDD sing 146 n n 
O6A H6A GDD sing 147 n n 
C21 O21 GDD sing 148 n n 
C21 C31 GDD sing 149 n n 
C21 H21 GDD sing 150 n n 
O21 HC GDD sing 151 n n 
C31 O31 GDD sing 152 n n 
C31 C41 GDD sing 153 n n 
C31 H31 GDD sing 154 n n 
O31 HD GDD sing 155 n n 
C41 O41 GDD sing 156 n n 
C41 H41 GDD sing 157 n n 
O41 HE GDD sing 158 n n 
#
_atom_sites.entry_id                     6Q94 
_atom_sites.fract_transf_matrix[1][1]    0.009841 
_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]    0.004328 
_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]    0.002605 
_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 2 NAP B 1 401 3 NAP NAP . 
J 3 GDD B 1 402 4 GDD GDD . 
K 2 NAP A 1 401 2 NAP NAP . 
L 3 GDD A 1 402 9 GDD GDD . 
M 2 NAP C 1 401 4 NAP NAP . 
N 3 GDD C 1 402 6 GDD GDD . 
O 2 NAP D 1 401 5 NAP NAP . 
P 3 GDD D 1 402 10 GDD GDD . 
Q 4 EDO D 1 403 1 EDO EDO . 
R 4 EDO D 1 404 3 EDO EDO . 
S 2 NAP E 1 401 6 NAP NAP . 
T 3 GDD E 1 402 7 GDD GDD . 
U 3 GDD F 1 401 5 GDD GDD . 
V 2 NAP F 1 402 7 NAP NAP . 
W 2 NAP G 1 401 8 NAP NAP . 
X 3 GDD G 1 402 11 GDD GDD . 
Y 4 EDO G 1 403 4 EDO EDO . 
Z 2 NAP H 1 401 9 NAP NAP . 
AA 3 GDD H 1 402 12 GDD GDD . 
BA 4 EDO H 1 403 2 EDO EDO . 
CA 5 HOH B 1 501 2 HOH HOH . 
DA 5 HOH C 1 501 4 HOH HOH . 
EA 5 HOH E 1 501 1 HOH HOH . 
FA 5 HOH G 1 501 3 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 N N2 GDD . . . AA 3 135.112 242.847 79.978 1 98.9 ? N2 GDD 402 H 1 
HETATM 2 C C2 GDD . . . AA 3 135.137 242.072 78.891 1 97.72 ? C2 GDD 402 H 1 
HETATM 3 N N1 GDD . . . AA 3 134.717 242.638 77.714 1 95.71 ? N1 GDD 402 H 1 
HETATM 4 N N3 GDD . . . AA 3 135.548 240.808 78.994 1 97.12 ? N3 GDD 402 H 1 
HETATM 5 C C4 GDD . . . AA 3 135.5 240.143 77.815 1 96.2 ? C4 GDD 402 H 1 
HETATM 6 C C5 GDD . . . AA 3 135.093 240.621 76.589 1 95.54 ? C5 GDD 402 H 1 
HETATM 7 C C6 GDD . . . AA 3 134.657 241.988 76.496 1 93.1 ? C6 GDD 402 H 1 
HETATM 8 O O6 GDD . . . AA 3 134.29 242.587 75.486 1 89 ? O6 GDD 402 H 1 
HETATM 9 N N7 GDD . . . AA 3 135.202 239.635 75.625 1 95.83 ? N7 GDD 402 H 1 
HETATM 10 C C8 GDD . . . AA 3 135.668 238.595 76.278 1 95.75 ? C8 GDD 402 H 1 
HETATM 11 N N9 GDD . . . AA 3 135.872 238.833 77.606 1 95.76 ? N9 GDD 402 H 1 
HETATM 12 C C1' GDD . . . AA 3 136.428 237.882 78.574 1 93.28 ? C1' GDD 402 H 1 
HETATM 13 C C2' GDD . . . AA 3 137.682 238.366 79.285 1 91.23 ? C2' GDD 402 H 1 
HETATM 14 O O2' GDD . . . AA 3 138.817 238.254 78.424 1 90.71 ? O2' GDD 402 H 1 
HETATM 15 C C3' GDD . . . AA 3 137.7 237.406 80.482 1 88.93 ? C3' GDD 402 H 1 
HETATM 16 O O3' GDD . . . AA 3 138.389 236.202 80.169 1 88.07 ? O3' GDD 402 H 1 
HETATM 17 C C4' GDD . . . AA 3 136.211 237.165 80.765 1 90.41 ? C4' GDD 402 H 1 
HETATM 18 O O4' GDD . . . AA 3 135.492 237.659 79.608 1 91.52 ? O4' GDD 402 H 1 
HETATM 19 C C5' GDD . . . AA 3 135.687 237.798 82.034 1 93.87 ? C5' GDD 402 H 1 
HETATM 20 O O5' GDD . . . AA 3 135.924 239.228 82.046 1 97.21 ? O5' GDD 402 H 1 
HETATM 21 P PA GDD . . . AA 3 135.406 240.236 83.24 1 100.61 ? PA GDD 402 H 1 
HETATM 22 O O1A GDD . . . AA 3 133.916 240.207 83.25 1 98.68 ? O1A GDD 402 H 1 
HETATM 23 O O2A GDD . . . AA 3 136.094 241.572 82.837 1 97.95 ? O2A GDD 402 H 1 
HETATM 24 O O3A GDD . . . AA 3 135.994 239.821 84.679 1 103.33 ? O3A GDD 402 H 1 
HETATM 25 P PB GDD . . . AA 3 137.319 239.106 85.236 1 102.96 ? PB GDD 402 H 1 
HETATM 26 O O2B GDD . . . AA 3 138.373 239.68 84.232 1 101.88 ? O2B GDD 402 H 1 
HETATM 27 O O3B GDD . . . AA 3 136.714 237.79 84.875 1 104.39 ? O3B GDD 402 H 1 
HETATM 28 O O1B GDD . . . AA 3 136.734 240.18 86.33 1 100.49 ? O1B GDD 402 H 1 
HETATM 29 C C11 GDD . . . AA 3 136.396 239.895 87.664 1 104.84 ? C11 GDD 402 H 1 
HETATM 30 O O51 GDD . . . AA 3 137.569 239.563 88.393 1 108.77 ? O51 GDD 402 H 1 
HETATM 31 C C51 GDD . . . AA 3 137.409 239.502 89.824 1 107.1 ? C51 GDD 402 H 1 
HETATM 32 C C61 GDD . . . AA 3 136.413 238.405 90.122 1 110.58 ? C61 GDD 402 H 1 
HETATM 33 O O6A GDD . . . AA 3 136.999 237.125 89.931 1 112.81 ? O6A GDD 402 H 1 
HETATM 34 C C21 GDD . . . AA 3 135.668 241.079 88.29 1 105.65 ? C21 GDD 402 H 1 
HETATM 35 O O21 GDD . . . AA 3 134.534 240.625 89.021 1 108.43 ? O21 GDD 402 H 1 
HETATM 36 C C31 GDD . . . AA 3 136.613 241.797 89.237 1 101.25 ? C31 GDD 402 H 1 
HETATM 37 O O31 GDD . . . AA 3 135.97 242.962 89.743 1 99.74 ? O31 GDD 402 H 1 
HETATM 38 C C41 GDD . . . AA 3 136.984 240.858 90.378 1 99.3 ? C41 GDD 402 H 1 
HETATM 39 O O41 GDD . . . AA 3 138.081 241.376 91.125 1 87.68 ? O41 GDD 402 H 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           48 
_model_server_stats.create_model_time_ms    259 
_model_server_stats.query_time_ms           368 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#