data_6DYD
#
_model_server_result.job_id            lDLQz7INW3LW-nFLsOOSXg 
_model_server_result.datetime_utc      '2024-11-15 22:02:32' 
_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          6dyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":202}' 
#
_entry.id    6DYD 
#
_exptl.entry_id    6DYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM ION' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.56 
_cell.angle_gamma         90 
_cell.entry_id            6DYD 
_cell.length_a            32.569 
_cell.length_b            87.77 
_cell.length_c            37.46 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,K 1 1 
B,F,G,H,I,J,L 2 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 D N N 
? 2 F N N 
? 2 G N N 
? 2 H 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
disulf ? disulf1 A SG CYS 96 A CYS 96 1_555 B SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
covale ? covale1 A SG CYS 98 A CYS 98 1_555 E CAB HEC . A HEC 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? 
covale ? covale2 A SG CYS 101 A CYS 101 1_555 E CAC HEC . A HEC 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? 
covale ? covale3 B SG CYS 98 C CYS 98 1_555 I CAB HEC . C HEC 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? 
covale ? covale4 B SG CYS 101 C CYS 101 1_555 I CAC HEC . C HEC 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? 
metalc ? metalc1 A O ALA 1 A ALA 1 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc2 A SD MET 7 A MET 7 1_555 E FE HEC . A HEC 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc3 A OD1 ASP 39 A ASP 39 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? 
metalc ? metalc4 A OD2 ASP 39 A ASP 39 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc5 A O THR 44 A THR 44 1_555 F CA CA . C CA 201 1_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc6 A O GLU 49 A GLU 49 1_555 G CA CA . C CA 202 1_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc7 A NE2 HIS 67 A HIS 67 1_555 J CU CU . C CU 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc8 A NE2 HIS 71 A HIS 71 1_555 J CU CU . C CU 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc9 A NE2 HIS 97 A HIS 97 1_555 J CU CU . C CU 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc10 A NE2 HIS 102 A HIS 102 1_555 E FE HEC . A HEC 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc11 C CA CA . A CA 201 1_555 K O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? 
metalc ? metalc12 C CA CA . A CA 201 1_555 K O HOH . A HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc13 C CA CA . A CA 201 1_555 K O HOH . A HOH 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? 
metalc ? metalc14 C CA CA . A CA 201 1_555 K O HOH . A HOH 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? 
metalc ? metalc15 C CA CA . A CA 201 1_555 K O HOH . A HOH 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc16 D CA CA . A CA 202 1_555 E O2D HEC . A HEC 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc17 D CA CA . A CA 202 1_555 K O HOH . A HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? 
metalc ? metalc18 D CA CA . A CA 202 1_555 L O HOH . C HOH 322 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.109 ? 
metalc ? metalc19 D CA CA . A CA 202 1_555 L O HOH . C HOH 340 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc20 K O HOH . A HOH 330 1_456 F CA CA . C CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc21 K O HOH . A HOH 340 1_456 G CA CA . C CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc22 B O ALA 1 C ALA 1 1_555 H CA CA . C CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc23 B OD1 ASP 2 C ASP 2 1_555 F CA CA . C CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc24 B OE2 GLU 4 C GLU 4 1_555 F CA CA . C CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc25 B SD MET 7 C MET 7 1_555 I FE HEC . C HEC 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc26 B OE2 GLU 8 C GLU 8 1_555 G CA CA . C CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc27 B OD1 ASP 39 C ASP 39 1_555 H CA CA . C CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? 
metalc ? metalc28 B OD2 ASP 39 C ASP 39 1_555 H CA CA . C CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? 
metalc ? metalc29 B NE2 HIS 67 C HIS 67 1_555 J CU CU . C CU 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc30 B NE2 HIS 71 C HIS 71 1_555 J CU CU . C CU 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc31 B NE2 HIS 102 C HIS 102 1_555 I FE HEC . C HEC 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc32 F CA CA . C CA 201 1_555 L O HOH . C HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? 
metalc ? metalc33 F CA CA . C CA 201 1_555 L O HOH . C HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc34 G CA CA . C CA 202 1_555 L O HOH . C HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
metalc ? metalc35 H CA CA . C CA 203 1_555 L O HOH . C HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.101 ? 
metalc ? metalc36 H CA CA . C CA 203 1_555 L O HOH . C HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc37 H CA CA . C CA 203 1_555 L O HOH . C HOH 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc38 H CA CA . C CA 203 1_555 L O HOH . C HOH 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
#
_chem_comp.formula           'Ca 2' 
_chem_comp.formula_weight    40.078 
_chem_comp.id                CA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CALCIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     6DYD 
_atom_sites.fract_transf_matrix[1][1]    0.030704 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002989 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011393 
_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]    0.026821 
_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 CA A 1 201 3 CA CA . 
D 2 CA A 1 202 5 CA CA . 
E 3 HEC A 1 203 2 HEC HEC . 
F 2 CA C 1 201 1 CA CA . 
G 2 CA C 1 202 2 CA CA . 
H 2 CA C 1 203 4 CA CA . 
I 3 HEC C 1 204 1 HEC HEC . 
J 4 CU C 1 205 1 CU CU . 
K 5 HOH A 1 301 44 HOH HOH . 
K 5 HOH A 2 302 23 HOH HOH . 
K 5 HOH A 3 303 118 HOH HOH . 
K 5 HOH A 4 304 95 HOH HOH . 
K 5 HOH A 5 305 50 HOH HOH . 
K 5 HOH A 6 306 29 HOH HOH . 
K 5 HOH A 7 307 64 HOH HOH . 
K 5 HOH A 8 308 113 HOH HOH . 
K 5 HOH A 9 309 80 HOH HOH . 
K 5 HOH A 10 310 57 HOH HOH . 
K 5 HOH A 11 311 49 HOH HOH . 
K 5 HOH A 12 312 66 HOH HOH . 
K 5 HOH A 13 313 147 HOH HOH . 
K 5 HOH A 14 314 86 HOH HOH . 
K 5 HOH A 15 315 155 HOH HOH . 
K 5 HOH A 16 316 16 HOH HOH . 
K 5 HOH A 17 317 8 HOH HOH . 
K 5 HOH A 18 318 140 HOH HOH . 
K 5 HOH A 19 319 33 HOH HOH . 
K 5 HOH A 20 320 160 HOH HOH . 
K 5 HOH A 21 321 32 HOH HOH . 
K 5 HOH A 22 322 28 HOH HOH . 
K 5 HOH A 23 323 153 HOH HOH . 
K 5 HOH A 24 324 9 HOH HOH . 
K 5 HOH A 25 325 119 HOH HOH . 
K 5 HOH A 26 326 11 HOH HOH . 
K 5 HOH A 27 327 18 HOH HOH . 
K 5 HOH A 28 328 98 HOH HOH . 
K 5 HOH A 29 329 78 HOH HOH . 
K 5 HOH A 30 330 61 HOH HOH . 
K 5 HOH A 31 331 79 HOH HOH . 
K 5 HOH A 32 332 89 HOH HOH . 
K 5 HOH A 33 333 92 HOH HOH . 
K 5 HOH A 34 334 17 HOH HOH . 
K 5 HOH A 35 335 38 HOH HOH . 
K 5 HOH A 36 336 5 HOH HOH . 
K 5 HOH A 37 337 93 HOH HOH . 
K 5 HOH A 38 338 10 HOH HOH . 
K 5 HOH A 39 339 127 HOH HOH . 
K 5 HOH A 40 340 62 HOH HOH . 
K 5 HOH A 41 341 3 HOH HOH . 
K 5 HOH A 42 342 51 HOH HOH . 
K 5 HOH A 43 343 82 HOH HOH . 
K 5 HOH A 44 344 84 HOH HOH . 
K 5 HOH A 45 345 116 HOH HOH . 
K 5 HOH A 46 346 56 HOH HOH . 
K 5 HOH A 47 347 85 HOH HOH . 
K 5 HOH A 48 348 100 HOH HOH . 
K 5 HOH A 49 349 55 HOH HOH . 
K 5 HOH A 50 350 137 HOH HOH . 
K 5 HOH A 51 351 148 HOH HOH . 
K 5 HOH A 52 352 65 HOH HOH . 
K 5 HOH A 53 353 106 HOH HOH . 
K 5 HOH A 54 354 91 HOH HOH . 
K 5 HOH A 55 355 142 HOH HOH . 
K 5 HOH A 56 356 12 HOH HOH . 
K 5 HOH A 57 357 108 HOH HOH . 
K 5 HOH A 58 358 88 HOH HOH . 
K 5 HOH A 59 359 107 HOH HOH . 
K 5 HOH A 60 360 59 HOH HOH . 
K 5 HOH A 61 361 154 HOH HOH . 
K 5 HOH A 62 362 13 HOH HOH . 
K 5 HOH A 63 363 152 HOH HOH . 
K 5 HOH A 64 364 20 HOH HOH . 
K 5 HOH A 65 365 139 HOH HOH . 
K 5 HOH A 66 366 99 HOH HOH . 
K 5 HOH A 67 367 104 HOH HOH . 
K 5 HOH A 68 368 63 HOH HOH . 
K 5 HOH A 69 369 146 HOH HOH . 
K 5 HOH A 70 370 138 HOH HOH . 
K 5 HOH A 71 371 130 HOH HOH . 
K 5 HOH A 72 372 68 HOH HOH . 
K 5 HOH A 73 373 115 HOH HOH . 
K 5 HOH A 74 374 35 HOH HOH . 
K 5 HOH A 75 375 123 HOH HOH . 
K 5 HOH A 76 376 37 HOH HOH . 
K 5 HOH A 77 377 58 HOH HOH . 
K 5 HOH A 78 378 48 HOH HOH . 
L 5 HOH C 1 301 74 HOH HOH . 
L 5 HOH C 2 302 131 HOH HOH . 
L 5 HOH C 3 303 97 HOH HOH . 
L 5 HOH C 4 304 103 HOH HOH . 
L 5 HOH C 5 305 124 HOH HOH . 
L 5 HOH C 6 306 67 HOH HOH . 
L 5 HOH C 7 307 47 HOH HOH . 
L 5 HOH C 8 308 81 HOH HOH . 
L 5 HOH C 9 309 128 HOH HOH . 
L 5 HOH C 10 310 83 HOH HOH . 
L 5 HOH C 11 311 121 HOH HOH . 
L 5 HOH C 12 312 117 HOH HOH . 
L 5 HOH C 13 313 45 HOH HOH . 
L 5 HOH C 14 314 60 HOH HOH . 
L 5 HOH C 15 315 42 HOH HOH . 
L 5 HOH C 16 316 24 HOH HOH . 
L 5 HOH C 17 317 30 HOH HOH . 
L 5 HOH C 18 318 41 HOH HOH . 
L 5 HOH C 19 319 19 HOH HOH . 
L 5 HOH C 20 320 70 HOH HOH . 
L 5 HOH C 21 321 112 HOH HOH . 
L 5 HOH C 22 322 114 HOH HOH . 
L 5 HOH C 23 323 36 HOH HOH . 
L 5 HOH C 24 324 150 HOH HOH . 
L 5 HOH C 25 325 43 HOH HOH . 
L 5 HOH C 26 326 31 HOH HOH . 
L 5 HOH C 27 327 26 HOH HOH . 
L 5 HOH C 28 328 144 HOH HOH . 
L 5 HOH C 29 329 40 HOH HOH . 
L 5 HOH C 30 330 7 HOH HOH . 
L 5 HOH C 31 331 14 HOH HOH . 
L 5 HOH C 32 332 111 HOH HOH . 
L 5 HOH C 33 333 53 HOH HOH . 
L 5 HOH C 34 334 6 HOH HOH . 
L 5 HOH C 35 335 34 HOH HOH . 
L 5 HOH C 36 336 126 HOH HOH . 
L 5 HOH C 37 337 27 HOH HOH . 
L 5 HOH C 38 338 102 HOH HOH . 
L 5 HOH C 39 339 46 HOH HOH . 
L 5 HOH C 40 340 122 HOH HOH . 
L 5 HOH C 41 341 69 HOH HOH . 
L 5 HOH C 42 342 158 HOH HOH . 
L 5 HOH C 43 343 71 HOH HOH . 
L 5 HOH C 44 344 151 HOH HOH . 
L 5 HOH C 45 345 135 HOH HOH . 
L 5 HOH C 46 346 21 HOH HOH . 
L 5 HOH C 47 347 76 HOH HOH . 
L 5 HOH C 48 348 15 HOH HOH . 
L 5 HOH C 49 349 156 HOH HOH . 
L 5 HOH C 50 350 157 HOH HOH . 
L 5 HOH C 51 351 159 HOH HOH . 
L 5 HOH C 52 352 134 HOH HOH . 
L 5 HOH C 53 353 96 HOH HOH . 
L 5 HOH C 54 354 125 HOH HOH . 
L 5 HOH C 55 355 72 HOH HOH . 
L 5 HOH C 56 356 132 HOH HOH . 
L 5 HOH C 57 357 4 HOH HOH . 
L 5 HOH C 58 358 101 HOH HOH . 
L 5 HOH C 59 359 120 HOH HOH . 
L 5 HOH C 60 360 161 HOH HOH . 
L 5 HOH C 61 361 39 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CA 
_atom_site.label_atom_id         CA 
_atom_site.label_comp_id         CA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         D 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               17.291 
_atom_site.Cartn_y               -6.054 
_atom_site.Cartn_z               5.095 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        48.52 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           202 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           252 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#