data_2GDF
#
_model_server_result.job_id            uyW05YUFC1P-ofC5TuVINw 
_model_server_result.datetime_utc      '2024-11-26 04:08:00' 
_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          2gdf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    2GDF 
#
_exptl.entry_id    2GDF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              54.938 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MANGANESE (II) ION' 
_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         120 
_cell.entry_id            2GDF 
_cell.length_a            72.938 
_cell.length_b            72.938 
_cell.length_c            161.362 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2GDF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 E 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 B OE2 GLU 8 B GLU 8 1_555 E MN MN . B MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc2 B OD2 ASP 10 B ASP 10 1_555 E MN MN . B MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc3 B OD2 ASP 10 B ASP 10 1_555 F CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? 
metalc ? metalc4 B OD1 ASP 10 B ASP 10 1_555 F CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc5 B O TYR 12 B TYR 12 1_555 F CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc6 B OD1 ASN 14 B ASN 14 1_555 F CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? 
metalc ? metalc7 B OD1 ASP 19 B ASP 19 1_555 E MN MN . B MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? 
metalc ? metalc8 B OD2 ASP 19 B ASP 19 1_555 F CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc9 B NE2 HIS 24 B HIS 24 1_555 E MN MN . B MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc10 E MN MN . B MN 301 1_555 J O HOH . B HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc11 F CA CA . B CA 302 1_555 J O HOH . B HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc12 D OE2 GLU 8 D GLU 8 1_555 G MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc13 D OD2 ASP 10 D ASP 10 1_555 G MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? 
metalc ? metalc14 D OD1 ASP 10 D ASP 10 1_555 H CA CA . D CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc15 D OD2 ASP 10 D ASP 10 1_555 H CA CA . D CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? 
metalc ? metalc16 D O TYR 12 D TYR 12 1_555 H CA CA . D CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc17 D OD1 ASN 14 D ASN 14 1_555 H CA CA . D CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
metalc ? metalc18 D OD1 ASP 19 D ASP 19 1_555 G MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc19 D OD2 ASP 19 D ASP 19 1_555 H CA CA . D CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc20 D NE2 HIS 24 D HIS 24 1_555 G MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc21 G MN MN . D MN 1301 1_555 L O HOH . D HOH 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc22 H CA CA . D CA 1302 1_555 L O HOH . D HOH 1314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
#
_chem_comp.formula           'Mn 2' 
_chem_comp.formula_weight    54.938 
_chem_comp.id                MN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MANGANESE (II) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     2GDF 
_atom_sites.fract_transf_matrix[1][1]    0.01371 
_atom_sites.fract_transf_matrix[1][2]    0.007916 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015831 
_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]    0.006197 
_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 2 MN B 1 301 301 MN MN . 
F 3 CA B 1 302 302 CA CA . 
G 2 MN D 1 1301 301 MN MN . 
H 3 CA D 1 1302 302 CA CA . 
I 4 HOH A 1 238 1 HOH HOH . 
I 4 HOH A 2 239 2 HOH HOH . 
I 4 HOH A 3 240 4 HOH HOH . 
I 4 HOH A 4 241 5 HOH HOH . 
I 4 HOH A 5 242 6 HOH HOH . 
I 4 HOH A 6 243 8 HOH HOH . 
I 4 HOH A 7 244 11 HOH HOH . 
I 4 HOH A 8 245 12 HOH HOH . 
I 4 HOH A 9 246 32 HOH HOH . 
I 4 HOH A 10 247 33 HOH HOH . 
I 4 HOH A 11 248 34 HOH HOH . 
I 4 HOH A 12 249 56 HOH HOH . 
I 4 HOH A 13 250 57 HOH HOH . 
I 4 HOH A 14 251 58 HOH HOH . 
I 4 HOH A 15 252 61 HOH HOH . 
I 4 HOH A 16 253 62 HOH HOH . 
I 4 HOH A 17 254 78 HOH HOH . 
I 4 HOH A 18 255 79 HOH HOH . 
I 4 HOH A 19 256 80 HOH HOH . 
I 4 HOH A 20 257 83 HOH HOH . 
I 4 HOH A 21 258 85 HOH HOH . 
I 4 HOH A 22 259 91 HOH HOH . 
I 4 HOH A 23 260 94 HOH HOH . 
I 4 HOH A 24 261 108 HOH HOH . 
I 4 HOH A 25 262 109 HOH HOH . 
I 4 HOH A 26 263 110 HOH HOH . 
I 4 HOH A 27 264 111 HOH HOH . 
I 4 HOH A 28 265 115 HOH HOH . 
I 4 HOH A 29 266 116 HOH HOH . 
I 4 HOH A 30 267 117 HOH HOH . 
I 4 HOH A 31 268 118 HOH HOH . 
I 4 HOH A 32 269 125 HOH HOH . 
I 4 HOH A 33 270 126 HOH HOH . 
I 4 HOH A 34 271 127 HOH HOH . 
I 4 HOH A 35 272 128 HOH HOH . 
I 4 HOH A 36 273 129 HOH HOH . 
I 4 HOH A 37 274 132 HOH HOH . 
I 4 HOH A 38 275 134 HOH HOH . 
I 4 HOH A 39 276 142 HOH HOH . 
I 4 HOH A 40 277 143 HOH HOH . 
I 4 HOH A 41 278 147 HOH HOH . 
I 4 HOH A 42 279 148 HOH HOH . 
J 4 HOH B 1 303 7 HOH HOH . 
J 4 HOH B 2 304 9 HOH HOH . 
J 4 HOH B 3 305 10 HOH HOH . 
J 4 HOH B 4 306 13 HOH HOH . 
J 4 HOH B 5 307 14 HOH HOH . 
J 4 HOH B 6 308 15 HOH HOH . 
J 4 HOH B 7 309 16 HOH HOH . 
J 4 HOH B 8 310 17 HOH HOH . 
J 4 HOH B 9 311 18 HOH HOH . 
J 4 HOH B 10 312 19 HOH HOH . 
J 4 HOH B 11 313 35 HOH HOH . 
J 4 HOH B 12 314 36 HOH HOH . 
J 4 HOH B 13 315 37 HOH HOH . 
J 4 HOH B 14 316 38 HOH HOH . 
J 4 HOH B 15 317 39 HOH HOH . 
J 4 HOH B 16 318 40 HOH HOH . 
J 4 HOH B 17 319 41 HOH HOH . 
J 4 HOH B 18 320 63 HOH HOH . 
J 4 HOH B 19 321 64 HOH HOH . 
J 4 HOH B 20 322 65 HOH HOH . 
J 4 HOH B 21 323 84 HOH HOH . 
J 4 HOH B 22 324 86 HOH HOH . 
J 4 HOH B 23 325 87 HOH HOH . 
J 4 HOH B 24 326 89 HOH HOH . 
J 4 HOH B 25 327 92 HOH HOH . 
J 4 HOH B 26 328 93 HOH HOH . 
J 4 HOH B 27 329 95 HOH HOH . 
J 4 HOH B 28 330 112 HOH HOH . 
J 4 HOH B 29 331 113 HOH HOH . 
J 4 HOH B 30 332 114 HOH HOH . 
J 4 HOH B 31 333 119 HOH HOH . 
J 4 HOH B 32 334 121 HOH HOH . 
J 4 HOH B 33 335 130 HOH HOH . 
J 4 HOH B 34 336 131 HOH HOH . 
J 4 HOH B 35 337 133 HOH HOH . 
J 4 HOH B 36 338 135 HOH HOH . 
J 4 HOH B 37 339 136 HOH HOH . 
J 4 HOH B 38 340 149 HOH HOH . 
J 4 HOH B 39 341 151 HOH HOH . 
K 4 HOH C 1 238 20 HOH HOH . 
K 4 HOH C 2 239 21 HOH HOH . 
K 4 HOH C 3 240 22 HOH HOH . 
K 4 HOH C 4 241 23 HOH HOH . 
K 4 HOH C 5 242 24 HOH HOH . 
K 4 HOH C 6 243 25 HOH HOH . 
K 4 HOH C 7 244 26 HOH HOH . 
K 4 HOH C 8 245 42 HOH HOH . 
K 4 HOH C 9 246 43 HOH HOH . 
K 4 HOH C 10 247 44 HOH HOH . 
K 4 HOH C 11 248 45 HOH HOH . 
K 4 HOH C 12 249 51 HOH HOH . 
K 4 HOH C 13 250 52 HOH HOH . 
K 4 HOH C 14 251 67 HOH HOH . 
K 4 HOH C 15 252 68 HOH HOH . 
K 4 HOH C 16 253 69 HOH HOH . 
K 4 HOH C 17 254 70 HOH HOH . 
K 4 HOH C 18 255 71 HOH HOH . 
K 4 HOH C 19 256 72 HOH HOH . 
K 4 HOH C 20 257 88 HOH HOH . 
K 4 HOH C 21 258 96 HOH HOH . 
K 4 HOH C 22 259 98 HOH HOH . 
K 4 HOH C 23 260 99 HOH HOH . 
K 4 HOH C 24 261 100 HOH HOH . 
K 4 HOH C 25 262 103 HOH HOH . 
K 4 HOH C 26 263 104 HOH HOH . 
K 4 HOH C 27 264 106 HOH HOH . 
K 4 HOH C 28 265 123 HOH HOH . 
K 4 HOH C 29 266 124 HOH HOH . 
K 4 HOH C 30 267 137 HOH HOH . 
K 4 HOH C 31 268 150 HOH HOH . 
K 4 HOH C 32 269 152 HOH HOH . 
K 4 HOH C 33 270 153 HOH HOH . 
L 4 HOH D 1 1303 3 HOH HOH . 
L 4 HOH D 2 1304 27 HOH HOH . 
L 4 HOH D 3 1305 28 HOH HOH . 
L 4 HOH D 4 1306 29 HOH HOH . 
L 4 HOH D 5 1307 30 HOH HOH . 
L 4 HOH D 6 1308 31 HOH HOH . 
L 4 HOH D 7 1309 46 HOH HOH . 
L 4 HOH D 8 1310 47 HOH HOH . 
L 4 HOH D 9 1311 48 HOH HOH . 
L 4 HOH D 10 1312 49 HOH HOH . 
L 4 HOH D 11 1313 50 HOH HOH . 
L 4 HOH D 12 1314 53 HOH HOH . 
L 4 HOH D 13 1315 54 HOH HOH . 
L 4 HOH D 14 1316 59 HOH HOH . 
L 4 HOH D 15 1317 73 HOH HOH . 
L 4 HOH D 16 1318 74 HOH HOH . 
L 4 HOH D 17 1319 76 HOH HOH . 
L 4 HOH D 18 1320 77 HOH HOH . 
L 4 HOH D 19 1321 81 HOH HOH . 
L 4 HOH D 20 1322 101 HOH HOH . 
L 4 HOH D 21 1323 102 HOH HOH . 
L 4 HOH D 22 1324 105 HOH HOH . 
L 4 HOH D 23 1325 107 HOH HOH . 
L 4 HOH D 24 1326 138 HOH HOH . 
L 4 HOH D 25 1327 139 HOH HOH . 
L 4 HOH D 26 1328 140 HOH HOH . 
L 4 HOH D 27 1329 141 HOH HOH . 
L 4 HOH D 28 1330 144 HOH HOH . 
L 4 HOH D 29 1331 145 HOH HOH . 
L 4 HOH D 30 1332 146 HOH HOH . 
L 4 HOH D 31 1333 154 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           MN 
_atom_site.label_atom_id         MN 
_atom_site.label_comp_id         MN 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         E 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               6.88 
_atom_site.Cartn_y               28.384 
_atom_site.Cartn_z               -17.963 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        38.69 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          MN 
_atom_site.auth_comp_id          MN 
_atom_site.auth_seq_id           301 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           229 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#