data_3VV4 # _model_server_result.job_id s220xPDCEB9QLjfehBgEEA _model_server_result.datetime_utc '2024-11-15 06:31:23' _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 3vv4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":201}' # _entry.id 3VV4 # _exptl.entry_id 3VV4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 588.694 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Phycoviolobilin,green light-absorbing form' _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 3VV4 _cell.length_a 72.868 _cell.length_b 72.868 _cell.length_c 166.667 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VV4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 ? dimeric 2 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,F,I 1 1 B,G,H,J 1 2 B,G,H,J 2 1 A,C,D,E,F,I 2 3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_545 -x+y,-x-1,z+1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 36.434 -63.105539 55.555667 3 'crystal symmetry operation' 2_444 -y-1,x-y-1,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -36.434 -63.105539 -55.555667 # 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 disulf ? disulf1 A SG CYS 99 A CYS 66 1_555 B SG CYS 99 B CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A SG CYS 127 A CYS 94 1_555 C C31 PVG . A PVG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale2 B SG CYS 127 B CYS 94 1_555 G C31 PVG . B PVG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? # _chem_comp.formula 'C33 H40 N4 O6' _chem_comp.formula_weight 588.694 _chem_comp.id PVG _chem_comp.mon_nstd_flag . _chem_comp.name 'Phycoviolobilin, green light-absorbing form' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3VV4 _atom_sites.fract_transf_matrix[1][1] 0.013723 _atom_sites.fract_transf_matrix[1][2] 0.007923 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015846 _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] 0.006 _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 PVG A 1 201 200 PVG PVG . D 3 SO4 A 1 202 1 SO4 SO4 . E 3 SO4 A 1 203 2 SO4 SO4 . F 3 SO4 A 1 204 3 SO4 SO4 . G 2 PVG B 1 201 200 PVG PVG . H 3 SO4 B 1 202 4 SO4 SO4 . I 4 HOH A 1 301 1 HOH HOH . I 4 HOH A 2 302 2 HOH HOH . I 4 HOH A 3 303 3 HOH HOH . I 4 HOH A 4 304 4 HOH HOH . I 4 HOH A 5 305 5 HOH HOH . I 4 HOH A 6 306 6 HOH HOH . I 4 HOH A 7 307 7 HOH HOH . I 4 HOH A 8 308 9 HOH HOH . I 4 HOH A 9 309 10 HOH HOH . I 4 HOH A 10 310 11 HOH HOH . I 4 HOH A 11 311 12 HOH HOH . I 4 HOH A 12 312 13 HOH HOH . I 4 HOH A 13 313 14 HOH HOH . I 4 HOH A 14 314 15 HOH HOH . I 4 HOH A 15 315 16 HOH HOH . I 4 HOH A 16 316 17 HOH HOH . I 4 HOH A 17 317 18 HOH HOH . I 4 HOH A 18 318 19 HOH HOH . I 4 HOH A 19 319 20 HOH HOH . I 4 HOH A 20 320 21 HOH HOH . I 4 HOH A 21 321 22 HOH HOH . I 4 HOH A 22 322 24 HOH HOH . I 4 HOH A 23 323 25 HOH HOH . I 4 HOH A 24 324 26 HOH HOH . I 4 HOH A 25 325 27 HOH HOH . I 4 HOH A 26 326 28 HOH HOH . I 4 HOH A 27 327 29 HOH HOH . I 4 HOH A 28 328 30 HOH HOH . I 4 HOH A 29 329 32 HOH HOH . I 4 HOH A 30 330 33 HOH HOH . I 4 HOH A 31 331 34 HOH HOH . I 4 HOH A 32 332 35 HOH HOH . I 4 HOH A 33 333 36 HOH HOH . I 4 HOH A 34 334 37 HOH HOH . I 4 HOH A 35 335 38 HOH HOH . I 4 HOH A 36 336 39 HOH HOH . I 4 HOH A 37 337 40 HOH HOH . I 4 HOH A 38 338 41 HOH HOH . I 4 HOH A 39 339 42 HOH HOH . I 4 HOH A 40 340 43 HOH HOH . I 4 HOH A 41 341 44 HOH HOH . I 4 HOH A 42 342 45 HOH HOH . I 4 HOH A 43 343 46 HOH HOH . I 4 HOH A 44 344 49 HOH HOH . I 4 HOH A 45 345 50 HOH HOH . I 4 HOH A 46 346 51 HOH HOH . I 4 HOH A 47 347 70 HOH HOH . I 4 HOH A 48 348 74 HOH HOH . I 4 HOH A 49 349 75 HOH HOH . I 4 HOH A 50 350 76 HOH HOH . I 4 HOH A 51 351 77 HOH HOH . I 4 HOH A 52 352 78 HOH HOH . I 4 HOH A 53 353 80 HOH HOH . I 4 HOH A 54 354 81 HOH HOH . I 4 HOH A 55 355 83 HOH HOH . I 4 HOH A 56 356 86 HOH HOH . I 4 HOH A 57 357 88 HOH HOH . I 4 HOH A 58 358 89 HOH HOH . I 4 HOH A 59 359 90 HOH HOH . I 4 HOH A 60 360 92 HOH HOH . I 4 HOH A 61 361 93 HOH HOH . I 4 HOH A 62 362 94 HOH HOH . I 4 HOH A 63 363 95 HOH HOH . I 4 HOH A 64 364 96 HOH HOH . I 4 HOH A 65 365 98 HOH HOH . I 4 HOH A 66 366 101 HOH HOH . I 4 HOH A 67 367 102 HOH HOH . I 4 HOH A 68 368 103 HOH HOH . I 4 HOH A 69 369 104 HOH HOH . I 4 HOH A 70 370 105 HOH HOH . I 4 HOH A 71 371 106 HOH HOH . I 4 HOH A 72 372 108 HOH HOH . I 4 HOH A 73 373 109 HOH HOH . I 4 HOH A 74 374 120 HOH HOH . I 4 HOH A 75 375 128 HOH HOH . I 4 HOH A 76 376 130 HOH HOH . I 4 HOH A 77 377 132 HOH HOH . I 4 HOH A 78 378 133 HOH HOH . I 4 HOH A 79 379 135 HOH HOH . J 4 HOH B 1 301 53 HOH HOH . J 4 HOH B 2 302 54 HOH HOH . J 4 HOH B 3 303 55 HOH HOH . J 4 HOH B 4 304 56 HOH HOH . J 4 HOH B 5 305 57 HOH HOH . J 4 HOH B 6 306 58 HOH HOH . J 4 HOH B 7 307 59 HOH HOH . J 4 HOH B 8 308 60 HOH HOH . J 4 HOH B 9 309 61 HOH HOH . J 4 HOH B 10 310 63 HOH HOH . J 4 HOH B 11 311 64 HOH HOH . J 4 HOH B 12 312 65 HOH HOH . J 4 HOH B 13 313 66 HOH HOH . J 4 HOH B 14 314 67 HOH HOH . J 4 HOH B 15 315 68 HOH HOH . J 4 HOH B 16 316 69 HOH HOH . J 4 HOH B 17 317 71 HOH HOH . J 4 HOH B 18 318 72 HOH HOH . J 4 HOH B 19 319 73 HOH HOH . J 4 HOH B 20 320 85 HOH HOH . J 4 HOH B 21 321 113 HOH HOH . J 4 HOH B 22 322 114 HOH HOH . J 4 HOH B 23 323 115 HOH HOH . J 4 HOH B 24 324 116 HOH HOH . J 4 HOH B 25 325 117 HOH HOH . J 4 HOH B 26 326 121 HOH HOH . J 4 HOH B 27 327 123 HOH HOH . J 4 HOH B 28 328 124 HOH HOH . J 4 HOH B 29 329 126 HOH HOH . J 4 HOH B 30 330 127 HOH HOH . J 4 HOH B 31 331 131 HOH HOH . J 4 HOH B 32 332 134 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 C32 PVG . . . G 2 -8.756 -35.704 -26.937 1 50.51 ? C32 PVG 201 B 1 HETATM 2 C C31 PVG . . . G 2 -7.981 -37.036 -26.865 1 52.81 ? C31 PVG 201 B 1 HETATM 3 C C3 PVG . . . G 2 -6.56 -36.955 -27.447 1 55.7 ? C3 PVG 201 B 1 HETATM 4 C C2 PVG . . . G 2 -5.432 -36.263 -27.019 1 55.71 ? C2 PVG 201 B 1 HETATM 5 C C21 PVG . . . G 2 -5.367 -35.207 -25.859 1 55.44 ? C21 PVG 201 B 1 HETATM 6 C C1 PVG . . . G 2 -4.378 -36.585 -27.901 1 55.38 ? C1 PVG 201 B 1 HETATM 7 O O1 PVG . . . G 2 -3.254 -36.116 -27.849 1 53.54 ? O1 PVG 201 B 1 HETATM 8 N N1 PVG . . . G 2 -4.762 -37.495 -28.826 1 55.58 ? N1 PVG 201 B 1 HETATM 9 C C4 PVG . . . G 2 -5.95 -38.072 -28.246 1 55.32 ? C4 PVG 201 B 1 HETATM 10 C C5 PVG . . . G 2 -6.342 -39.514 -28.242 1 52.26 ? C5 PVG 201 B 1 HETATM 11 C C6 PVG . . . G 2 -5.953 -40.232 -29.513 1 48.1 ? C6 PVG 201 B 1 HETATM 12 N N2 PVG . . . G 2 -6.779 -40.43 -30.546 1 47.84 ? N2 PVG 201 B 1 HETATM 13 C C7 PVG . . . G 2 -4.768 -40.92 -29.76 1 47.42 ? C7 PVG 201 B 1 HETATM 14 C C41 PVG . . . G 2 -3.511 -40.968 -28.802 1 45.85 ? C41 PVG 201 B 1 HETATM 15 C C8 PVG . . . G 2 -4.865 -41.499 -30.998 1 44.58 ? C8 PVG 201 B 1 HETATM 16 C C51 PVG . . . G 2 -3.795 -42.357 -31.684 1 49.54 ? C51 PVG 201 B 1 HETATM 17 C C52 PVG . . . G 2 -3.865 -43.783 -31.141 1 55.52 ? C52 PVG 201 B 1 HETATM 18 C C53 PVG . . . G 2 -3.024 -44.735 -31.989 1 58.67 ? C53 PVG 201 B 1 HETATM 19 O O55 PVG . . . G 2 -3.56 -45.26 -32.977 1 67.92 ? O55 PVG 201 B 1 HETATM 20 O O54 PVG . . . G 2 -1.871 -44.939 -31.618 1 68.22 ? O54 PVG 201 B 1 HETATM 21 C C9 PVG . . . G 2 -6.175 -41.209 -31.459 1 44.62 ? C9 PVG 201 B 1 HETATM 22 C C10 PVG . . . G 2 -6.639 -41.604 -32.721 1 44.01 ? C10 PVG 201 B 1 HETATM 23 C C11 PVG . . . G 2 -7.778 -40.958 -33.221 1 45.1 ? C11 PVG 201 B 1 HETATM 24 N N3 PVG . . . G 2 -8.46 -39.892 -32.729 1 42.93 ? N3 PVG 201 B 1 HETATM 25 C C12 PVG . . . G 2 -8.408 -41.38 -34.411 1 42.18 ? C12 PVG 201 B 1 HETATM 26 C C61 PVG . . . G 2 -7.968 -42.516 -35.354 1 42.01 ? C61 PVG 201 B 1 HETATM 27 C C62 PVG . . . G 2 -8.985 -43.685 -35.361 1 36.89 ? C62 PVG 201 B 1 HETATM 28 C C63 PVG . . . G 2 -8.951 -44.455 -34.028 1 42.86 ? C63 PVG 201 B 1 HETATM 29 O O65 PVG . . . G 2 -10.018 -44.446 -33.325 1 42.75 ? O65 PVG 201 B 1 HETATM 30 O O64 PVG . . . G 2 -7.837 -44.929 -33.68 1 44.91 ? O64 PVG 201 B 1 HETATM 31 C C13 PVG . . . G 2 -9.497 -40.534 -34.581 1 44.19 ? C13 PVG 201 B 1 HETATM 32 C C71 PVG . . . G 2 -10.448 -40.619 -35.814 1 37.93 ? C71 PVG 201 B 1 HETATM 33 C C14 PVG . . . G 2 -9.499 -39.583 -33.507 1 43.69 ? C14 PVG 201 B 1 HETATM 34 C C15 PVG . . . G 2 -10.369 -38.494 -33.366 1 42.32 ? C15 PVG 201 B 1 HETATM 35 C C16 PVG . . . G 2 -11.777 -38.424 -33.441 1 44.17 ? C16 PVG 201 B 1 HETATM 36 C C17 PVG . . . G 2 -12.672 -39.53 -33.311 1 44.22 ? C17 PVG 201 B 1 HETATM 37 C C81 PVG . . . G 2 -12.306 -41.002 -33.034 1 48.58 ? C81 PVG 201 B 1 HETATM 38 C C18 PVG . . . G 2 -13.974 -39.031 -33.392 1 44.83 ? C18 PVG 201 B 1 HETATM 39 C C91 PVG . . . G 2 -15.29 -39.76 -33.332 1 48.45 ? C91 PVG 201 B 1 HETATM 40 C C92 PVG . . . G 2 -15.331 -40.906 -34.364 1 50.77 ? C92 PVG 201 B 1 HETATM 41 C C19 PVG . . . G 2 -13.821 -37.65 -33.609 1 46.95 ? C19 PVG 201 B 1 HETATM 42 O O19 PVG . . . G 2 -14.751 -36.861 -33.751 1 44.52 ? O19 PVG 201 B 1 HETATM 43 N N4 PVG . . . G 2 -12.535 -37.304 -33.615 1 42.43 ? N4 PVG 201 B 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 43 #