data_1HH4
#
_model_server_result.job_id            JOo475ULNzOT42YuEMvajQ 
_model_server_result.datetime_utc      '2024-10-24 04:33:13' 
_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          1hh4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1190}' 
#
_entry.id    1HH4 
#
_exptl.entry_id    1HH4 
_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    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            1HH4 
_cell.length_a            154.7 
_cell.length_b            88.7 
_cell.length_c            62.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1HH4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PQS dimeric 2 author_and_software_defined_assembly 1 
PQS dimeric 2 author_and_software_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,F,I,K,M 1 1 
B,D,G,H,J,L,N 2 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 E N N 
? 3 G 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 NZ LYS 16 A LYS 16 1_555 F MG MG . A MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? 
metalc ? metalc2 A OG1 THR 17 A THR 17 1_555 F MG MG . A MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc3 A O THR 35 A THR 35 1_555 F MG MG . A MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? 
metalc ? metalc4 A OD2 ASP 57 A ASP 57 1_555 F MG MG . A MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? 
metalc ? metalc5 A OD1 ASP 57 A ASP 57 1_555 F MG MG . A MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? 
metalc ? metalc6 E O2B GDP . A GDP 1190 1_555 F MG MG . A MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? 
metalc ? metalc7 F MG MG . A MG 1191 1_555 K O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? 
metalc ? metalc8 B OG1 THR 17 B THR 17 1_555 H MG MG . B MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc9 B OD1 ASP 57 B ASP 57 1_555 H MG MG . B MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc10 B OD2 ASP 57 B ASP 57 1_555 H MG MG . B MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
metalc ? metalc11 G O2B GDP . B GDP 1190 1_555 H MG MG . B MG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? 
metalc ? metalc12 H MG MG . B MG 1191 1_555 L O HOH . B HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
#
_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                     1HH4 
_atom_sites.fract_transf_matrix[1][1]    0.006464 
_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]    0.011274 
_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]    0.015974 
_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 3 GDP A 1 1190 1190 GDP GDP . 
F 4 MG A 1 1191 1191 MG MG . 
G 3 GDP B 1 1190 1190 GDP GDP . 
H 4 MG B 1 1191 1191 MG MG . 
I 5 GER D 1 1502 1502 GER GER . 
J 5 GER E 1 1503 1503 GER GER . 
K 6 HOH A 1 2001 2001 HOH HOH . 
K 6 HOH A 2 2002 2002 HOH HOH . 
K 6 HOH A 3 2003 2003 HOH HOH . 
K 6 HOH A 4 2004 2004 HOH HOH . 
K 6 HOH A 5 2005 2005 HOH HOH . 
K 6 HOH A 6 2006 2006 HOH HOH . 
K 6 HOH A 7 2007 2007 HOH HOH . 
K 6 HOH A 8 2008 2008 HOH HOH . 
K 6 HOH A 9 2009 2009 HOH HOH . 
K 6 HOH A 10 2010 2010 HOH HOH . 
K 6 HOH A 11 2011 2011 HOH HOH . 
K 6 HOH A 12 2012 2012 HOH HOH . 
L 6 HOH B 1 2001 2001 HOH HOH . 
L 6 HOH B 2 2002 2002 HOH HOH . 
L 6 HOH B 3 2003 2003 HOH HOH . 
L 6 HOH B 4 2004 2004 HOH HOH . 
L 6 HOH B 5 2005 2005 HOH HOH . 
L 6 HOH B 6 2006 2006 HOH HOH . 
M 6 HOH D 1 2001 2001 HOH HOH . 
M 6 HOH D 2 2002 2002 HOH HOH . 
M 6 HOH D 3 2003 2003 HOH HOH . 
M 6 HOH D 4 2004 2004 HOH HOH . 
M 6 HOH D 5 2005 2005 HOH HOH . 
M 6 HOH D 6 2006 2006 HOH HOH . 
M 6 HOH D 7 2007 2007 HOH HOH . 
N 6 HOH E 1 2001 2001 HOH HOH . 
N 6 HOH E 2 2002 2002 HOH HOH . 
N 6 HOH E 3 2003 2003 HOH HOH . 
N 6 HOH E 4 2004 2004 HOH HOH . 
N 6 HOH E 5 2005 2005 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 . . . G 3 43.444 67.056 63.048 1 48.11 ? PB GDP 1190 B 1 
HETATM 2 O O1B GDP . . . G 3 44.314 68.215 63.332 1 48.11 ? O1B GDP 1190 B 1 
HETATM 3 O O2B GDP . . . G 3 43.998 65.988 62.352 1 48.11 ? O2B GDP 1190 B 1 
HETATM 4 O O3B GDP . . . G 3 42.723 66.613 64.434 1 48.11 ? O3B GDP 1190 B 1 
HETATM 5 O O3A GDP . . . G 3 42.294 67.593 62.086 1 48.11 ? O3A GDP 1190 B 1 
HETATM 6 P PA GDP . . . G 3 41.745 67.068 60.571 1 48.11 ? PA GDP 1190 B 1 
HETATM 7 O O1A GDP . . . G 3 42.822 67.205 59.552 1 48.11 ? O1A GDP 1190 B 1 
HETATM 8 O O2A GDP . . . G 3 41.237 65.657 60.773 1 48.11 ? O2A GDP 1190 B 1 
HETATM 9 O O5' GDP . . . G 3 40.635 68.129 60.31 1 48.11 ? O5' GDP 1190 B 1 
HETATM 10 C C5' GDP . . . G 3 39.367 68.137 61.051 1 48.11 ? C5' GDP 1190 B 1 
HETATM 11 C C4' GDP . . . G 3 38.159 68.347 60.24 1 48.11 ? C4' GDP 1190 B 1 
HETATM 12 O O4' GDP . . . G 3 38.221 69.692 59.591 1 48.11 ? O4' GDP 1190 B 1 
HETATM 13 C C3' GDP . . . G 3 38.007 67.383 58.997 1 48.11 ? C3' GDP 1190 B 1 
HETATM 14 O O3' GDP . . . G 3 36.611 66.905 59.019 1 48.11 ? O3' GDP 1190 B 1 
HETATM 15 C C2' GDP . . . G 3 38.248 68.192 57.684 1 48.11 ? C2' GDP 1190 B 1 
HETATM 16 O O2' GDP . . . G 3 37.398 67.963 56.546 1 48.11 ? O2' GDP 1190 B 1 
HETATM 17 C C1' GDP . . . G 3 38.128 69.668 58.104 1 48.11 ? C1' GDP 1190 B 1 
HETATM 18 N N9 GDP . . . G 3 39.196 70.553 57.607 1 48.11 ? N9 GDP 1190 B 1 
HETATM 19 C C8 GDP . . . G 3 40.625 70.176 57.854 1 48.11 ? C8 GDP 1190 B 1 
HETATM 20 N N7 GDP . . . G 3 41.114 71.33 57.209 1 48.11 ? N7 GDP 1190 B 1 
HETATM 21 C C5 GDP . . . G 3 40.299 72.229 56.674 1 48.11 ? C5 GDP 1190 B 1 
HETATM 22 C C6 GDP . . . G 3 40.193 73.455 55.981 1 48.11 ? C6 GDP 1190 B 1 
HETATM 23 O O6 GDP . . . G 3 41.351 74.057 55.68 1 48.11 ? O6 GDP 1190 B 1 
HETATM 24 N N1 GDP . . . G 3 39.016 74.041 55.617 1 48.11 ? N1 GDP 1190 B 1 
HETATM 25 C C2 GDP . . . G 3 37.739 73.321 55.982 1 48.11 ? C2 GDP 1190 B 1 
HETATM 26 N N2 GDP . . . G 3 36.712 74.029 55.553 1 48.11 ? N2 GDP 1190 B 1 
HETATM 27 N N3 GDP . . . G 3 37.795 72.229 56.605 1 48.11 ? N3 GDP 1190 B 1 
HETATM 28 C C4 GDP . . . G 3 38.968 71.696 56.939 1 48.11 ? C4 GDP 1190 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#