data_2WVM
#
_model_server_result.job_id            iyovQb3lNl6bsLWU96fCgg 
_model_server_result.datetime_utc      '2024-11-27 00:56:05' 
_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          2wvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":400}' 
#
_entry.id    2WVM 
#
_exptl.entry_id    2WVM 
_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            2WVM 
_cell.length_a            112.766 
_cell.length_b            112.766 
_cell.length_c            199.69 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2WVM 
_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 
_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 F 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc2 A OE2 GLU 19 A GLU 19 1_555 E ZN ZN . A ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc3 A OE1 GLU 19 A GLU 19 1_555 E ZN ZN . A ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc4 A OD2 ASP 169 A ASP 169 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc5 A OE1 GLU 292 A GLU 292 6_544 I ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc6 A NE2 HIS 296 A HIS 296 6_544 I ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc7 C O2B GDD . A GDD 400 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? 
metalc ? metalc8 C O1A GDD . A GDD 400 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc9 E ZN ZN . A ZN 1392 1_555 J O HOH . A HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc10 E ZN ZN . A ZN 1392 1_555 B NE2 HIS 105 B HIS 105 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? 
metalc ? metalc11 B NE2 HIS 8 B HIS 8 1_555 H ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc12 B OE1 GLU 19 B GLU 19 1_555 H ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc13 B OD1 ASP 169 B ASP 169 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? 
metalc ? metalc14 B OD2 ASP 169 B ASP 169 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? 
metalc ? metalc15 B OD1 ASP 242 B ASP 242 1_555 H ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc16 B OD2 ASP 242 B ASP 242 1_555 H ZN ZN . B ZN 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc17 B OE2 GLU 292 B GLU 292 1_555 I ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc18 B OE1 GLU 292 B GLU 292 1_555 I ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? 
metalc ? metalc19 B NE2 HIS 296 B HIS 296 1_555 I ZN ZN . B ZN 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc20 F O1A GDD . B GDD 400 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc21 F O2B GDD . B GDD 400 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? 
metalc ? metalc22 H ZN ZN . B ZN 1392 1_555 K O HOH . B HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
#
_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                     2WVM 
_atom_sites.fract_transf_matrix[1][1]    0.008868 
_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]    0.008868 
_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]    0.005008 
_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 2 GDD B 1 400 400 GDD GDD . 
G 3 MG B 1 401 401 MG MG . 
H 4 ZN B 1 1392 1392 ZN ZN . 
I 4 ZN B 1 1393 1393 ZN ZN . 
J 5 HOH A 1 2001 2001 HOH HOH . 
J 5 HOH A 2 2002 2002 HOH HOH . 
J 5 HOH A 3 2003 2003 HOH HOH . 
J 5 HOH A 4 2004 2004 HOH HOH . 
J 5 HOH A 5 2005 2005 HOH HOH . 
J 5 HOH A 6 2006 2006 HOH HOH . 
J 5 HOH A 7 2007 2007 HOH HOH . 
K 5 HOH B 1 2001 2001 HOH HOH . 
K 5 HOH B 2 2002 2002 HOH HOH . 
K 5 HOH B 3 2003 2003 HOH HOH . 
K 5 HOH B 4 2004 2004 HOH HOH . 
K 5 HOH B 5 2005 2005 HOH HOH . 
K 5 HOH B 6 2006 2006 HOH HOH . 
K 5 HOH B 7 2007 2007 HOH HOH . 
K 5 HOH B 8 2008 2008 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 . . . F 2 16.535 -7.486 -13.783 1 46.72 ? N2 GDD 400 B 1 
HETATM 2 C C2 GDD . . . F 2 16.732 -6.108 -14.269 1 74.82 ? C2 GDD 400 B 1 
HETATM 3 N N1 GDD . . . F 2 17.907 -5.442 -14.066 1 47.35 ? N1 GDD 400 B 1 
HETATM 4 N N3 GDD . . . F 2 15.689 -5.554 -14.914 1 42.69 ? N3 GDD 400 B 1 
HETATM 5 C C4 GDD . . . F 2 15.812 -4.297 -15.397 1 57.37 ? C4 GDD 400 B 1 
HETATM 6 C C5 GDD . . . F 2 16.991 -3.589 -15.226 1 48.08 ? C5 GDD 400 B 1 
HETATM 7 C C6 GDD . . . F 2 18.055 -4.188 -14.544 1 45.63 ? C6 GDD 400 B 1 
HETATM 8 O O6 GDD . . . F 2 19.233 -3.532 -14.356 1 82.44 ? O6 GDD 400 B 1 
HETATM 9 N N7 GDD . . . F 2 16.793 -2.379 -15.792 1 68.44 ? N7 GDD 400 B 1 
HETATM 10 C C8 GDD . . . F 2 15.542 -2.347 -16.302 1 80.09 ? C8 GDD 400 B 1 
HETATM 11 N N9 GDD . . . F 2 14.962 -3.53 -16.065 1 39.79 ? N9 GDD 400 B 1 
HETATM 12 C C1' GDD . . . F 2 13.586 -3.956 -16.37 1 49.94 ? C1' GDD 400 B 1 
HETATM 13 C C2' GDD . . . F 2 12.65 -2.748 -16.392 1 55.09 ? C2' GDD 400 B 1 
HETATM 14 O O2' GDD . . . F 2 11.952 -2.51 -15.167 1 66.74 ? O2' GDD 400 B 1 
HETATM 15 C C3' GDD . . . F 2 11.698 -3.125 -17.488 1 67.48 ? C3' GDD 400 B 1 
HETATM 16 O O3' GDD . . . F 2 10.685 -4.006 -16.958 1 60.57 ? O3' GDD 400 B 1 
HETATM 17 C C4' GDD . . . F 2 12.649 -3.829 -18.445 1 64.18 ? C4' GDD 400 B 1 
HETATM 18 O O4' GDD . . . F 2 13.535 -4.58 -17.644 1 66.43 ? O4' GDD 400 B 1 
HETATM 19 C C5' GDD . . . F 2 13.51 -2.8 -19.147 1 48.24 ? C5' GDD 400 B 1 
HETATM 20 O O5' GDD . . . F 2 12.596 -1.817 -19.586 1 58.4 ? O5' GDD 400 B 1 
HETATM 21 P PA GDD . . . F 2 13.05 -0.299 -19.706 1 50.1 ? PA GDD 400 B 1 
HETATM 22 O O1A GDD . . . F 2 11.751 0.492 -19.919 1 118.81 ? O1A GDD 400 B 1 
HETATM 23 O O2A GDD . . . F 2 14.078 -0.035 -18.656 1 41.01 ? O2A GDD 400 B 1 
HETATM 24 O O3A GDD . . . F 2 13.888 -0.314 -21.052 1 56.05 ? O3A GDD 400 B 1 
HETATM 25 P PB GDD . . . F 2 13.332 0.571 -22.259 1 44.07 ? PB GDD 400 B 1 
HETATM 26 O O2B GDD . . . F 2 11.837 0.735 -22.057 1 165.71 ? O2B GDD 400 B 1 
HETATM 27 O O3B GDD . . . F 2 14.239 1.745 -22.453 1 52.09 ? O3B GDD 400 B 1 
HETATM 28 O O1B GDD . . . F 2 13.62 -0.384 -23.515 1 44.66 ? O1B GDD 400 B 1 
HETATM 29 C C11 GDD . . . F 2 12.992 -1.646 -23.575 1 35.21 ? C11 GDD 400 B 1 
HETATM 30 O O51 GDD . . . F 2 12.357 -1.851 -24.843 1 82.2 ? O51 GDD 400 B 1 
HETATM 31 C C51 GDD . . . F 2 13.209 -1.863 -26 1 32.56 ? C51 GDD 400 B 1 
HETATM 32 C C61 GDD . . . F 2 12.387 -2.316 -27.197 1 46.22 ? C61 GDD 400 B 1 
HETATM 33 O O6A GDD . . . F 2 11.215 -2.969 -26.709 1 80.52 ? O6A GDD 400 B 1 
HETATM 34 C C21 GDD . . . F 2 14.083 -2.673 -23.328 1 52.42 ? C21 GDD 400 B 1 
HETATM 35 O O21 GDD . . . F 2 13.469 -3.941 -23.13 1 44.26 ? O21 GDD 400 B 1 
HETATM 36 C C31 GDD . . . F 2 15.079 -2.794 -24.473 1 52.31 ? C31 GDD 400 B 1 
HETATM 37 O O31 GDD . . . F 2 15.729 -4.07 -24.336 1 63.82 ? O31 GDD 400 B 1 
HETATM 38 C C41 GDD . . . F 2 14.428 -2.78 -25.852 1 56.56 ? C41 GDD 400 B 1 
HETATM 39 O O41 GDD . . . F 2 15.453 -2.402 -26.781 1 82.78 ? O41 GDD 400 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#