data_2WVL
#
_model_server_result.job_id            PxkSPqeeCQQl4HpYTXbgiA 
_model_server_result.datetime_utc      '2024-11-02 01:30:40' 
_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          2wvl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":400}' 
#
_entry.id    2WVL 
#
_exptl.entry_id    2WVL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              605.341 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_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            2WVL 
_cell.length_a            113.456 
_cell.length_b            113.456 
_cell.length_c            195.982 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2WVL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 2 C N N 
? 2 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 ND1 HIS 8 A HIS 8 1_555 E ZN ZN . A ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc2 A OE2 GLU 19 A GLU 19 1_555 E ZN ZN . A ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc3 A OE1 GLU 19 A GLU 19 1_555 E ZN ZN . A ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc4 A OD2 ASP 169 A ASP 169 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc5 A OE1 GLU 251 A GLU 251 1_555 F ZN ZN . A ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc6 A OE1 GLU 292 A GLU 292 5_645 K ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc7 A NE2 HIS 296 A HIS 296 5_645 K ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc8 A ND1 HIS 309 A HIS 309 1_555 F ZN ZN . A ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc9 A NE2 HIS 311 A HIS 311 1_555 F ZN ZN . A ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc10 C O1A GDD . A GDD 400 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc11 C O2B GDD . A GDD 400 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc12 E ZN ZN . A ZN 1392 1_555 L O HOH . A HOH 2016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc13 E ZN ZN . A ZN 1392 1_555 B NE2 HIS 105 B HIS 105 8_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? 
metalc ? metalc14 B NE2 HIS 8 B HIS 8 1_555 I ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc15 B OE1 GLU 19 B GLU 19 1_555 I ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc16 B OD2 ASP 169 B ASP 169 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? 
metalc ? metalc17 B OD2 ASP 242 B ASP 242 1_555 I ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc18 B OD1 ASP 242 B ASP 242 1_555 I ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc19 B OE1 GLU 251 B GLU 251 1_555 J ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc20 B OE2 GLU 292 B GLU 292 1_555 K ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc21 B OE1 GLU 292 B GLU 292 1_555 K ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc22 B NE2 HIS 296 B HIS 296 1_555 K ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc23 B NE2 HIS 311 B HIS 311 1_555 J ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc24 G O2B GDD . B GDD 400 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? 
metalc ? metalc25 G O1A GDD . B GDD 400 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc26 J ZN ZN . B ZN 1393 1_555 M O HOH . B HOH 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
#
_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 83 n n 
N2 H2N1 GDD sing 84 n n 
N2 H2N2 GDD sing 85 n n 
C2 N1 GDD sing 86 n n 
C2 N3 GDD doub 87 n n 
N1 C6 GDD sing 88 n n 
N1 H1 GDD sing 89 n n 
N3 C4 GDD sing 90 n n 
C4 C5 GDD doub 91 n y 
C4 N9 GDD sing 92 n y 
C5 C6 GDD sing 93 n n 
C5 N7 GDD sing 94 n y 
C6 O6 GDD doub 95 n n 
N7 C8 GDD doub 96 n y 
C8 N9 GDD sing 97 n y 
C8 H8 GDD sing 98 n n 
N9 C1' GDD sing 99 n n 
C1' C2' GDD sing 100 n n 
C1' O4' GDD sing 101 n n 
C1' H1' GDD sing 102 n n 
C2' O2' GDD sing 103 n n 
C2' C3' GDD sing 104 n n 
C2' H2' GDD sing 105 n n 
O2' HA GDD sing 106 n n 
C3' O3' GDD sing 107 n n 
C3' C4' GDD sing 108 n n 
C3' H3' GDD sing 109 n n 
O3' HB GDD sing 110 n n 
C4' O4' GDD sing 111 n n 
C4' C5' GDD sing 112 n n 
C4' H4' GDD sing 113 n n 
C5' O5' GDD sing 114 n n 
C5' "H5'1" GDD sing 115 n n 
C5' "H5'2" GDD sing 116 n n 
O5' PA GDD sing 117 n n 
PA O1A GDD doub 118 n n 
PA O2A GDD sing 119 n n 
PA O3A GDD sing 120 n n 
O2A HO2A GDD sing 121 n n 
O3A PB GDD sing 122 n n 
PB O2B GDD sing 123 n n 
PB O3B GDD doub 124 n n 
PB O1B GDD sing 125 n n 
O2B HO2B GDD sing 126 n n 
O1B C11 GDD sing 127 n n 
C11 O51 GDD sing 128 n n 
C11 C21 GDD sing 129 n n 
C11 H11 GDD sing 130 n n 
O51 C51 GDD sing 131 n n 
C51 C61 GDD sing 132 n n 
C51 C41 GDD sing 133 n n 
C51 H51 GDD sing 134 n n 
C61 O6A GDD sing 135 n n 
C61 H611 GDD sing 136 n n 
C61 H612 GDD sing 137 n n 
O6A H6A GDD sing 138 n n 
C21 O21 GDD sing 139 n n 
C21 C31 GDD sing 140 n n 
C21 H21 GDD sing 141 n n 
O21 HC GDD sing 142 n n 
C31 O31 GDD sing 143 n n 
C31 C41 GDD sing 144 n n 
C31 H31 GDD sing 145 n n 
O31 HD GDD sing 146 n n 
C41 O41 GDD sing 147 n n 
C41 H41 GDD sing 148 n n 
O41 HE GDD sing 149 n n 
#
_atom_sites.entry_id                     2WVL 
_atom_sites.fract_transf_matrix[1][1]    0.008814 
_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]    0.008814 
_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]    0.005103 
_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
C 2 GDD A 1 400 400 GDD GDD . 
D 3 MG A 1 401 401 MG MG . 
E 4 ZN A 1 1392 1392 ZN ZN . 
F 4 ZN A 1 1393 1393 ZN ZN . 
G 2 GDD B 1 400 400 GDD GDD . 
H 3 MG B 1 401 401 MG MG . 
I 4 ZN B 1 1392 1392 ZN ZN . 
J 4 ZN B 1 1393 1393 ZN ZN . 
K 4 ZN B 1 1394 1394 ZN ZN . 
L 5 HOH A 1 2001 2001 HOH HOH . 
L 5 HOH A 2 2002 2002 HOH HOH . 
L 5 HOH A 3 2003 2003 HOH HOH . 
L 5 HOH A 4 2004 2004 HOH HOH . 
L 5 HOH A 5 2005 2005 HOH HOH . 
L 5 HOH A 6 2006 2006 HOH HOH . 
L 5 HOH A 7 2007 2007 HOH HOH . 
L 5 HOH A 8 2008 2008 HOH HOH . 
L 5 HOH A 9 2009 2009 HOH HOH . 
L 5 HOH A 10 2010 2010 HOH HOH . 
L 5 HOH A 11 2011 2011 HOH HOH . 
L 5 HOH A 12 2012 2012 HOH HOH . 
L 5 HOH A 13 2013 2013 HOH HOH . 
L 5 HOH A 14 2014 2014 HOH HOH . 
L 5 HOH A 15 2015 2015 HOH HOH . 
L 5 HOH A 16 2016 2016 HOH HOH . 
L 5 HOH A 17 2017 2017 HOH HOH . 
M 5 HOH B 1 2001 2001 HOH HOH . 
M 5 HOH B 2 2002 2002 HOH HOH . 
M 5 HOH B 3 2003 2003 HOH HOH . 
M 5 HOH B 4 2004 2004 HOH HOH . 
M 5 HOH B 5 2005 2005 HOH HOH . 
M 5 HOH B 6 2006 2006 HOH HOH . 
M 5 HOH B 7 2007 2007 HOH HOH . 
M 5 HOH B 8 2008 2008 HOH HOH . 
M 5 HOH B 9 2009 2009 HOH HOH . 
M 5 HOH B 10 2010 2010 HOH HOH . 
M 5 HOH B 11 2011 2011 HOH HOH . 
M 5 HOH B 12 2012 2012 HOH HOH . 
M 5 HOH B 13 2013 2013 HOH HOH . 
M 5 HOH B 14 2014 2014 HOH HOH . 
M 5 HOH B 15 2015 2015 HOH HOH . 
M 5 HOH B 16 2016 2016 HOH HOH . 
M 5 HOH B 17 2017 2017 HOH HOH . 
M 5 HOH B 18 2018 2018 HOH HOH . 
M 5 HOH B 19 2019 2019 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 . . . G 2 105.914 -16.187 35.955 1 65.36 ? N2 GDD 400 B 1 
HETATM 2 C C2 GDD . . . G 2 107.283 -16.429 35.426 1 50.15 ? C2 GDD 400 B 1 
HETATM 3 N N1 GDD . . . G 2 107.896 -17.63 35.61 1 76.02 ? N1 GDD 400 B 1 
HETATM 4 N N3 GDD . . . G 2 107.916 -15.429 34.776 1 49.27 ? N3 GDD 400 B 1 
HETATM 5 C C4 GDD . . . G 2 109.164 -15.631 34.282 1 74.42 ? C4 GDD 400 B 1 
HETATM 6 C C5 GDD . . . G 2 109.81 -16.845 34.451 1 88.38 ? C5 GDD 400 B 1 
HETATM 7 C C6 GDD . . . G 2 109.144 -17.86 35.141 1 58.45 ? C6 GDD 400 B 1 
HETATM 8 O O6 GDD . . . G 2 109.712 -19.075 35.348 1 79.88 ? O6 GDD 400 B 1 
HETATM 9 N N7 GDD . . . G 2 111.02 -16.726 33.863 1 68.19 ? N7 GDD 400 B 1 
HETATM 10 C C8 GDD . . . G 2 111.109 -15.477 33.344 1 75.83 ? C8 GDD 400 B 1 
HETATM 11 N N9 GDD . . . G 2 109.968 -14.824 33.605 1 76.56 ? N9 GDD 400 B 1 
HETATM 12 C C1' GDD . . . G 2 109.579 -13.431 33.272 1 41.17 ? C1' GDD 400 B 1 
HETATM 13 C C2' GDD . . . G 2 110.799 -12.532 33.098 1 106.47 ? C2' GDD 400 B 1 
HETATM 14 O O2' GDD . . . G 2 111.207 -11.856 34.299 1 74.54 ? O2' GDD 400 B 1 
HETATM 15 C C3' GDD . . . G 2 110.326 -11.596 32.004 1 94.67 ? C3' GDD 400 B 1 
HETATM 16 O O3' GDD . . . G 2 109.476 -10.566 32.521 1 93.34 ? O3' GDD 400 B 1 
HETATM 17 C C4' GDD . . . G 2 109.485 -12.526 31.146 1 67.72 ? C4' GDD 400 B 1 
HETATM 18 O O4' GDD . . . G 2 108.824 -13.384 32.063 1 75.31 ? O4' GDD 400 B 1 
HETATM 19 C C5' GDD . . . G 2 110.355 -13.375 30.238 1 51.8 ? C5' GDD 400 B 1 
HETATM 20 O O5' GDD . . . G 2 111.461 -12.578 29.832 1 123.12 ? O5' GDD 400 B 1 
HETATM 21 P PA GDD . . . G 2 112.982 -13.088 29.938 1 68.4 ? PA GDD 400 B 1 
HETATM 22 O O1A GDD . . . G 2 113.803 -11.818 29.718 1 116.89 ? O1A GDD 400 B 1 
HETATM 23 O O2A GDD . . . G 2 113.128 -13.987 31.135 1 85.26 ? O2A GDD 400 B 1 
HETATM 24 O O3A GDD . . . G 2 113.06 -14.035 28.632 1 72.88 ? O3A GDD 400 B 1 
HETATM 25 P PB GDD . . . G 2 113.838 -13.509 27.302 1 74.58 ? PB GDD 400 B 1 
HETATM 26 O O2B GDD . . . G 2 114.056 -12.003 27.44 1 69.1 ? O2B GDD 400 B 1 
HETATM 27 O O3B GDD . . . G 2 114.944 -14.504 26.963 1 51.66 ? O3B GDD 400 B 1 
HETATM 28 O O1B GDD . . . G 2 112.801 -13.644 26.098 1 73.93 ? O1B GDD 400 B 1 
HETATM 29 C C11 GDD . . . G 2 111.642 -12.845 26.141 1 62.82 ? C11 GDD 400 B 1 
HETATM 30 O O51 GDD . . . G 2 111.547 -12.035 24.966 1 114.19 ? O51 GDD 400 B 1 
HETATM 31 C C51 GDD . . . G 2 111.413 -12.679 23.697 1 41.4 ? C51 GDD 400 B 1 
HETATM 32 C C61 GDD . . . G 2 110.802 -11.568 22.833 1 84.62 ? C61 GDD 400 B 1 
HETATM 33 O O6A GDD . . . G 2 109.801 -12.021 21.883 1 58.78 ? O6A GDD 400 B 1 
HETATM 34 C C21 GDD . . . G 2 110.546 -13.877 26.264 1 86.66 ? C21 GDD 400 B 1 
HETATM 35 O O21 GDD . . . G 2 109.281 -13.23 26.376 1 62.96 ? O21 GDD 400 B 1 
HETATM 36 C C31 GDD . . . G 2 110.64 -14.782 25.053 1 57.85 ? C31 GDD 400 B 1 
HETATM 37 O O31 GDD . . . G 2 109.586 -15.734 25.2 1 68.95 ? O31 GDD 400 B 1 
HETATM 38 C C41 GDD . . . G 2 110.531 -13.952 23.761 1 99.43 ? C41 GDD 400 B 1 
HETATM 39 O O41 GDD . . . G 2 110.852 -14.779 22.639 1 40.95 ? O41 GDD 400 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#