data_2WVL
#
_model_server_result.job_id            T93vDyBRhAP5Wko64RDujQ 
_model_server_result.datetime_utc      '2024-11-23 11:33:54' 
_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":"C","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 . . . C 2 114.13 25.559 13.451 1 84.35 ? N2 GDD 400 A 1 
HETATM 2 C C2 GDD . . . C 2 115.461 25.133 13.958 1 95.59 ? C2 GDD 400 A 1 
HETATM 3 N N1 GDD . . . C 2 116.514 25.978 13.834 1 70.28 ? N1 GDD 400 A 1 
HETATM 4 N N3 GDD . . . C 2 115.603 23.911 14.536 1 44.77 ? N3 GDD 400 A 1 
HETATM 5 C C4 GDD . . . C 2 116.827 23.524 15 1 137.85 ? C4 GDD 400 A 1 
HETATM 6 C C5 GDD . . . C 2 117.916 24.381 14.875 1 44.41 ? C5 GDD 400 A 1 
HETATM 7 C C6 GDD . . . C 2 117.742 25.629 14.275 1 79.76 ? C6 GDD 400 A 1 
HETATM 8 O O6 GDD . . . C 2 118.781 26.501 14.122 1 66.64 ? O6 GDD 400 A 1 
HETATM 9 N N7 GDD . . . C 2 118.976 23.744 15.4 1 102.68 ? N7 GDD 400 A 1 
HETATM 10 C C8 GDD . . . C 2 118.561 22.543 15.854 1 58.78 ? C8 GDD 400 A 1 
HETATM 11 N N9 GDD . . . C 2 117.257 22.404 15.6 1 71.73 ? N9 GDD 400 A 1 
HETATM 12 C C1' GDD . . . C 2 116.397 21.233 15.917 1 77.57 ? C1' GDD 400 A 1 
HETATM 13 C C2' GDD . . . C 2 117.129 19.881 15.991 1 78.41 ? C2' GDD 400 A 1 
HETATM 14 O O2' GDD . . . C 2 116.873 18.945 14.927 1 61.95 ? O2' GDD 400 A 1 
HETATM 15 C C3' GDD . . . C 2 116.618 19.287 17.278 1 91.09 ? C3' GDD 400 A 1 
HETATM 16 O O3' GDD . . . C 2 115.439 18.513 17.018 1 64.13 ? O3' GDD 400 A 1 
HETATM 17 C C4' GDD . . . C 2 116.296 20.509 18.121 1 105.06 ? C4' GDD 400 A 1 
HETATM 18 O O4' GDD . . . C 2 115.84 21.496 17.205 1 111.42 ? O4' GDD 400 A 1 
HETATM 19 C C5' GDD . . . C 2 117.565 20.983 18.821 1 47.94 ? C5' GDD 400 A 1 
HETATM 20 O O5' GDD . . . C 2 118.13 19.775 19.311 1 90.86 ? O5' GDD 400 A 1 
HETATM 21 P PA GDD . . . C 2 119.699 19.457 19.437 1 90.59 ? PA GDD 400 A 1 
HETATM 22 O O1A GDD . . . C 2 119.702 17.967 19.707 1 72.97 ? O1A GDD 400 A 1 
HETATM 23 O O2A GDD . . . C 2 120.529 20.042 18.297 1 71.89 ? O2A GDD 400 A 1 
HETATM 24 O O3A GDD . . . C 2 120.052 20.277 20.788 1 83.15 ? O3A GDD 400 A 1 
HETATM 25 P PB GDD . . . C 2 120.552 19.541 22.139 1 64.56 ? PB GDD 400 A 1 
HETATM 26 O O2B GDD . . . C 2 120.07 18.106 22.094 1 161.36 ? O2B GDD 400 A 1 
HETATM 27 O O3B GDD . . . C 2 122.05 19.806 22.264 1 73.79 ? O3B GDD 400 A 1 
HETATM 28 O O1B GDD . . . C 2 119.731 20.233 23.368 1 52.18 ? O1B GDD 400 A 1 
HETATM 29 C C11 GDD . . . C 2 118.294 20.126 23.519 1 57.74 ? C11 GDD 400 A 1 
HETATM 30 O O51 GDD . . . C 2 117.835 19.531 24.758 1 117.97 ? O51 GDD 400 A 1 
HETATM 31 C C51 GDD . . . C 2 117.963 20.268 25.997 1 41.83 ? C51 GDD 400 A 1 
HETATM 32 C C61 GDD . . . C 2 117.299 19.437 27.135 1 133.25 ? C61 GDD 400 A 1 
HETATM 33 O O6A GDD . . . C 2 116.21 20.034 27.911 1 50.51 ? O6A GDD 400 A 1 
HETATM 34 C C21 GDD . . . C 2 117.681 21.504 23.32 1 34.34 ? C21 GDD 400 A 1 
HETATM 35 O O21 GDD . . . C 2 116.288 21.405 23.039 1 62.65 ? O21 GDD 400 A 1 
HETATM 36 C C31 GDD . . . C 2 117.93 22.401 24.522 1 122.31 ? C31 GDD 400 A 1 
HETATM 37 O O31 GDD . . . C 2 117.251 23.636 24.241 1 71.35 ? O31 GDD 400 A 1 
HETATM 38 C C41 GDD . . . C 2 117.495 21.741 25.844 1 88.7 ? C41 GDD 400 A 1 
HETATM 39 O O41 GDD . . . C 2 118.032 22.515 26.928 1 90.1 ? O41 GDD 400 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           39 
#