data_4B8Z
#
_model_server_result.job_id            -ePRcxhsL30qtvxV9R6zmQ 
_model_server_result.datetime_utc      '2024-11-24 02:52:08' 
_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          4b8z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":901}' 
#
_entry.id    4B8Z 
#
_exptl.entry_id    4B8Z 
_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            4B8Z 
_cell.length_a            91.447 
_cell.length_b            91.447 
_cell.length_c            429.13 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4B8Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 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,E,F,M 1 1 
B,G,H,N 2 1 
C,I,J,O 3 1 
D,K,L,P 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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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                     4B8Z 
_atom_sites.fract_transf_matrix[1][1]    0.010935 
_atom_sites.fract_transf_matrix[1][2]    0.006313 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012627 
_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]    0.00233 
_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
E 2 NAP A 1 900 900 NAP NAP . 
F 3 GDP A 1 901 901 GDP GDP . 
G 2 NAP B 1 900 900 NAP NAP . 
H 3 GDP B 1 901 901 GDP GDP . 
I 2 NAP C 1 900 900 NAP NAP . 
J 3 GDP C 1 901 901 GDP GDP . 
K 2 NAP D 1 900 900 NAP NAP . 
L 3 GDP D 1 901 901 GDP GDP . 
M 4 HOH A 1 2001 2001 HOH HOH . 
M 4 HOH A 2 2002 2002 HOH HOH . 
M 4 HOH A 3 2003 2003 HOH HOH . 
N 4 HOH B 1 2001 2001 HOH HOH . 
N 4 HOH B 2 2002 2002 HOH HOH . 
N 4 HOH B 3 2003 2003 HOH HOH . 
N 4 HOH B 4 2004 2004 HOH HOH . 
N 4 HOH B 5 2005 2005 HOH HOH . 
N 4 HOH B 6 2006 2006 HOH HOH . 
N 4 HOH B 7 2007 2007 HOH HOH . 
O 4 HOH C 1 2001 2001 HOH HOH . 
O 4 HOH C 2 2002 2002 HOH HOH . 
O 4 HOH C 3 2003 2003 HOH HOH . 
O 4 HOH C 4 2004 2004 HOH HOH . 
O 4 HOH C 5 2005 2005 HOH HOH . 
P 4 HOH D 1 2001 2001 HOH HOH . 
P 4 HOH D 2 2002 2002 HOH HOH . 
P 4 HOH D 3 2003 2003 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 . . . L 3 21.121 22.946 -69.705 1 63.75 ? PB GDP 901 D 1 
HETATM 2 O O1B GDP . . . L 3 21.493 21.956 -70.814 1 60.8 ? O1B GDP 901 D 1 
HETATM 3 O O2B GDP . . . L 3 21.308 24.366 -70.23 1 62.72 ? O2B GDP 901 D 1 
HETATM 4 O O3B GDP . . . L 3 21.838 22.704 -68.428 1 63.87 ? O3B GDP 901 D 1 
HETATM 5 O O3A GDP . . . L 3 19.569 22.893 -69.38 1 67.5 ? O3A GDP 901 D 1 
HETATM 6 P PA GDP . . . L 3 18.478 21.901 -68.799 1 67.95 ? PA GDP 901 D 1 
HETATM 7 O O1A GDP . . . L 3 18.236 22.303 -67.39 1 69.26 ? O1A GDP 901 D 1 
HETATM 8 O O2A GDP . . . L 3 17.232 21.956 -69.677 1 66.29 ? O2A GDP 901 D 1 
HETATM 9 O O5' GDP . . . L 3 19.176 20.48 -68.847 1 69.29 ? O5' GDP 901 D 1 
HETATM 10 C C5' GDP . . . L 3 19.26 19.715 -70.069 1 69.97 ? C5' GDP 901 D 1 
HETATM 11 C C4' GDP . . . L 3 19.919 18.384 -69.803 1 69.86 ? C4' GDP 901 D 1 
HETATM 12 O O4' GDP . . . L 3 19.126 17.611 -68.872 1 72.47 ? O4' GDP 901 D 1 
HETATM 13 C C3' GDP . . . L 3 20.091 17.495 -71.029 1 69.07 ? C3' GDP 901 D 1 
HETATM 14 O O3' GDP . . . L 3 21.279 16.729 -70.876 1 68.74 ? O3' GDP 901 D 1 
HETATM 15 C C2' GDP . . . L 3 18.822 16.64 -71 1 70 ? C2' GDP 901 D 1 
HETATM 16 O O2' GDP . . . L 3 18.973 15.427 -71.727 1 67.81 ? O2' GDP 901 D 1 
HETATM 17 C C1' GDP . . . L 3 18.66 16.425 -69.493 1 72.57 ? C1' GDP 901 D 1 
HETATM 18 N N9 GDP . . . L 3 17.274 16.168 -69.04 1 75.36 ? N9 GDP 901 D 1 
HETATM 19 C C8 GDP . . . L 3 16.802 14.988 -68.523 1 76.78 ? C8 GDP 901 D 1 
HETATM 20 N N7 GDP . . . L 3 15.54 15.03 -68.166 1 78.16 ? N7 GDP 901 D 1 
HETATM 21 C C5 GDP . . . L 3 15.147 16.322 -68.468 1 77.73 ? C5 GDP 901 D 1 
HETATM 22 C C6 GDP . . . L 3 13.883 16.984 -68.318 1 78.85 ? C6 GDP 901 D 1 
HETATM 23 O O6 GDP . . . L 3 12.845 16.5 -67.881 1 79.22 ? O6 GDP 901 D 1 
HETATM 24 N N1 GDP . . . L 3 13.923 18.299 -68.746 1 80.13 ? N1 GDP 901 D 1 
HETATM 25 C C2 GDP . . . L 3 15.029 18.931 -69.262 1 78.46 ? C2 GDP 901 D 1 
HETATM 26 N N2 GDP . . . L 3 14.885 20.21 -69.61 1 78.24 ? N2 GDP 901 D 1 
HETATM 27 N N3 GDP . . . L 3 16.214 18.334 -69.416 1 76.27 ? N3 GDP 901 D 1 
HETATM 28 C C4 GDP . . . L 3 16.207 17.041 -69.006 1 76.53 ? C4 GDP 901 D 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#