data_3DV4
#
_model_server_result.job_id            7KKfvmjhYEh-6sM9GgOizQ 
_model_server_result.datetime_utc      '2024-11-26 13:09:16' 
_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          3dv4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":114}' 
#
_entry.id    3DV4 
#
_exptl.entry_id    3DV4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              238.192 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' 
_entity.pdbx_number_of_molecules    1 
_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            3DV4 
_cell.length_a            72.51 
_cell.length_b            72.51 
_cell.length_c            85.91 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DV4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 A SG CYS 23 A CYS 23 1_555 A SG CYS 94 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
disulf ? disulf2 B SG CYS 22 B CYS 22 1_555 B SG CYS 98 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
#
_chem_comp.formula           'C8 H14 O8' 
_chem_comp.formula_weight    238.192 
_chem_comp.id                KDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     '3-deoxy-d-manno-oct-2-ulopyranosonic acid;2-keto-3-deoxy-D-mannooctanoic acid;3-deoxy-alpha-D-manno-oct-2-ulosonic acid;3-deoxy-D-manno-oct-2-ulosonic acid;3-deoxy-manno-oct-2-ulosonic acid' 
#
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
C1 O1A KDO doub 152 n n 
C1 O1B KDO sing 153 n n 
C1 C2 KDO sing 154 n n 
O1B HO1B KDO sing 155 n n 
C2 O2 KDO sing 156 n n 
C2 C3 KDO sing 157 n n 
C2 O6 KDO sing 158 n n 
O2 HO2 KDO sing 159 n n 
C3 C4 KDO sing 160 n n 
C3 H31 KDO sing 161 n n 
C3 H32 KDO sing 162 n n 
C4 O4 KDO sing 163 n n 
C4 C5 KDO sing 164 n n 
C4 H4 KDO sing 165 n n 
O4 HO4 KDO sing 166 n n 
C5 O5 KDO sing 167 n n 
C5 C6 KDO sing 168 n n 
C5 H5 KDO sing 169 n n 
O5 HO5 KDO sing 170 n n 
C6 O6 KDO sing 171 n n 
C6 C7 KDO sing 172 n n 
C6 H6 KDO sing 173 n n 
C7 O7 KDO sing 174 n n 
C7 C8 KDO sing 175 n n 
C7 H7 KDO sing 176 n n 
O7 HO7 KDO sing 177 n n 
C8 O8 KDO sing 178 n n 
C8 H81 KDO sing 179 n n 
C8 H82 KDO sing 180 n n 
O8 HO8 KDO sing 181 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
KDO DKdopa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
KDO a-D-Kdop 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
KDO Kdo 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     3DV4 
_atom_sites.fract_transf_matrix[1][1]    0.013791 
_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]    0.013791 
_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]    0.01164 
_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 3 MG A 1 115 115 MG MG . 
D 4 KDO B 1 114 114 KDO KDO . 
E 5 PG4 B 1 116 116 PG4 PG4 . 
F 6 HOH A 1 116 1 HOH HOH . 
F 6 HOH A 2 117 2 HOH HOH . 
F 6 HOH A 3 118 3 HOH HOH . 
F 6 HOH A 4 119 4 HOH HOH . 
F 6 HOH A 5 120 5 HOH HOH . 
F 6 HOH A 6 121 6 HOH HOH . 
F 6 HOH A 7 122 8 HOH HOH . 
F 6 HOH A 8 123 9 HOH HOH . 
F 6 HOH A 9 124 11 HOH HOH . 
F 6 HOH A 10 125 14 HOH HOH . 
F 6 HOH A 11 126 15 HOH HOH . 
F 6 HOH A 12 127 16 HOH HOH . 
F 6 HOH A 13 128 17 HOH HOH . 
F 6 HOH A 14 129 19 HOH HOH . 
F 6 HOH A 15 130 21 HOH HOH . 
F 6 HOH A 16 131 22 HOH HOH . 
F 6 HOH A 17 132 23 HOH HOH . 
F 6 HOH A 18 133 24 HOH HOH . 
F 6 HOH A 19 134 25 HOH HOH . 
F 6 HOH A 20 135 26 HOH HOH . 
F 6 HOH A 21 136 27 HOH HOH . 
F 6 HOH A 22 137 29 HOH HOH . 
F 6 HOH A 23 138 30 HOH HOH . 
F 6 HOH A 24 139 35 HOH HOH . 
F 6 HOH A 25 140 36 HOH HOH . 
F 6 HOH A 26 141 38 HOH HOH . 
F 6 HOH A 27 142 39 HOH HOH . 
F 6 HOH A 28 143 45 HOH HOH . 
F 6 HOH A 29 144 46 HOH HOH . 
F 6 HOH A 30 145 47 HOH HOH . 
F 6 HOH A 31 146 48 HOH HOH . 
F 6 HOH A 32 147 49 HOH HOH . 
F 6 HOH A 33 148 51 HOH HOH . 
F 6 HOH A 34 149 52 HOH HOH . 
F 6 HOH A 35 150 53 HOH HOH . 
F 6 HOH A 36 151 54 HOH HOH . 
F 6 HOH A 37 152 56 HOH HOH . 
F 6 HOH A 38 153 57 HOH HOH . 
F 6 HOH A 39 154 59 HOH HOH . 
F 6 HOH A 40 155 61 HOH HOH . 
F 6 HOH A 41 156 62 HOH HOH . 
F 6 HOH A 42 157 65 HOH HOH . 
F 6 HOH A 43 158 66 HOH HOH . 
F 6 HOH A 44 159 67 HOH HOH . 
F 6 HOH A 45 160 68 HOH HOH . 
F 6 HOH A 46 161 70 HOH HOH . 
F 6 HOH A 47 162 71 HOH HOH . 
F 6 HOH A 48 163 72 HOH HOH . 
F 6 HOH A 49 164 74 HOH HOH . 
F 6 HOH A 50 165 75 HOH HOH . 
F 6 HOH A 51 166 77 HOH HOH . 
F 6 HOH A 52 167 82 HOH HOH . 
F 6 HOH A 53 168 83 HOH HOH . 
F 6 HOH A 54 169 86 HOH HOH . 
F 6 HOH A 55 170 89 HOH HOH . 
F 6 HOH A 56 171 91 HOH HOH . 
F 6 HOH A 57 172 92 HOH HOH . 
F 6 HOH A 58 173 93 HOH HOH . 
F 6 HOH A 59 174 97 HOH HOH . 
F 6 HOH A 60 175 98 HOH HOH . 
F 6 HOH A 61 176 99 HOH HOH . 
F 6 HOH A 62 177 101 HOH HOH . 
F 6 HOH A 63 178 102 HOH HOH . 
F 6 HOH A 64 179 103 HOH HOH . 
F 6 HOH A 65 180 107 HOH HOH . 
F 6 HOH A 66 181 108 HOH HOH . 
F 6 HOH A 67 182 109 HOH HOH . 
F 6 HOH A 68 183 110 HOH HOH . 
F 6 HOH A 69 184 112 HOH HOH . 
F 6 HOH A 70 185 116 HOH HOH . 
F 6 HOH A 71 186 117 HOH HOH . 
F 6 HOH A 72 187 118 HOH HOH . 
F 6 HOH A 73 188 121 HOH HOH . 
F 6 HOH A 74 189 125 HOH HOH . 
F 6 HOH A 75 190 127 HOH HOH . 
G 6 HOH B 1 117 7 HOH HOH . 
G 6 HOH B 2 118 10 HOH HOH . 
G 6 HOH B 3 119 12 HOH HOH . 
G 6 HOH B 4 120 13 HOH HOH . 
G 6 HOH B 5 121 18 HOH HOH . 
G 6 HOH B 6 122 20 HOH HOH . 
G 6 HOH B 7 123 28 HOH HOH . 
G 6 HOH B 8 124 31 HOH HOH . 
G 6 HOH B 9 125 32 HOH HOH . 
G 6 HOH B 10 126 33 HOH HOH . 
G 6 HOH B 11 127 34 HOH HOH . 
G 6 HOH B 12 128 37 HOH HOH . 
G 6 HOH B 13 129 40 HOH HOH . 
G 6 HOH B 14 130 41 HOH HOH . 
G 6 HOH B 15 131 42 HOH HOH . 
G 6 HOH B 16 132 43 HOH HOH . 
G 6 HOH B 17 133 44 HOH HOH . 
G 6 HOH B 18 134 55 HOH HOH . 
G 6 HOH B 19 135 58 HOH HOH . 
G 6 HOH B 20 136 60 HOH HOH . 
G 6 HOH B 21 137 63 HOH HOH . 
G 6 HOH B 22 138 64 HOH HOH . 
G 6 HOH B 23 139 69 HOH HOH . 
G 6 HOH B 24 140 73 HOH HOH . 
G 6 HOH B 25 141 76 HOH HOH . 
G 6 HOH B 26 142 78 HOH HOH . 
G 6 HOH B 27 143 79 HOH HOH . 
G 6 HOH B 28 144 80 HOH HOH . 
G 6 HOH B 29 145 81 HOH HOH . 
G 6 HOH B 30 146 84 HOH HOH . 
G 6 HOH B 31 147 85 HOH HOH . 
G 6 HOH B 32 148 87 HOH HOH . 
G 6 HOH B 33 149 88 HOH HOH . 
G 6 HOH B 34 150 90 HOH HOH . 
G 6 HOH B 35 151 94 HOH HOH . 
G 6 HOH B 36 152 95 HOH HOH . 
G 6 HOH B 37 153 96 HOH HOH . 
G 6 HOH B 38 154 100 HOH HOH . 
G 6 HOH B 39 155 104 HOH HOH . 
G 6 HOH B 40 156 105 HOH HOH . 
G 6 HOH B 41 157 106 HOH HOH . 
G 6 HOH B 42 158 111 HOH HOH . 
G 6 HOH B 43 159 113 HOH HOH . 
G 6 HOH B 44 160 114 HOH HOH . 
G 6 HOH B 45 161 115 HOH HOH . 
G 6 HOH B 46 162 119 HOH HOH . 
G 6 HOH B 47 163 120 HOH HOH . 
G 6 HOH B 48 164 122 HOH HOH . 
G 6 HOH B 49 165 123 HOH HOH . 
G 6 HOH B 50 166 124 HOH HOH . 
G 6 HOH B 51 167 126 HOH HOH . 
G 6 HOH B 52 168 128 HOH HOH . 
G 6 HOH B 53 169 129 HOH HOH . 
G 6 HOH B 54 170 130 HOH HOH . 
G 6 HOH B 55 171 131 HOH HOH . 
G 6 HOH B 56 172 132 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 C C1 KDO . . . D 4 14.644 -12.913 10.456 1 38.22 ? C1 KDO 114 B 1 
HETATM 2 O O1A KDO . . . D 4 14.209 -14.088 10.465 1 36.33 ? O1A KDO 114 B 1 
HETATM 3 O O1B KDO . . . D 4 14.818 -12.276 11.519 1 42.37 ? O1B KDO 114 B 1 
HETATM 4 C C2 KDO . . . D 4 14.308 -12.079 9.249 1 41.15 ? C2 KDO 114 B 1 
HETATM 5 O O2 KDO . . . D 4 14.194 -10.717 9.671 1 32.99 ? O2 KDO 114 B 1 
HETATM 6 C C3 KDO . . . D 4 15.388 -12.172 8.181 1 37.48 ? C3 KDO 114 B 1 
HETATM 7 C C4 KDO . . . D 4 15.056 -11.125 7.125 1 34.52 ? C4 KDO 114 B 1 
HETATM 8 O O4 KDO . . . D 4 15.996 -11.218 6.055 1 39.1 ? O4 KDO 114 B 1 
HETATM 9 C C5 KDO . . . D 4 13.654 -11.381 6.591 1 37.73 ? C5 KDO 114 B 1 
HETATM 10 O O5 KDO . . . D 4 13.705 -12.607 5.865 1 34.99 ? O5 KDO 114 B 1 
HETATM 11 C C6 KDO . . . D 4 12.616 -11.532 7.701 1 38.11 ? C6 KDO 114 B 1 
HETATM 12 O O6 KDO . . . D 4 13.076 -12.484 8.659 1 45.05 ? O6 KDO 114 B 1 
HETATM 13 C C7 KDO . . . D 4 11.313 -12.054 7.108 1 39.17 ? C7 KDO 114 B 1 
HETATM 14 O O7 KDO . . . D 4 11.129 -11.493 5.801 1 37.82 ? O7 KDO 114 B 1 
HETATM 15 C C8 KDO . . . D 4 10.124 -11.687 7.984 1 37.64 ? C8 KDO 114 B 1 
HETATM 16 O O8 KDO . . . D 4 9.959 -10.267 7.978 1 41.55 ? O8 KDO 114 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           237 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           16 
#