data_6RVB # _model_server_result.job_id Vn873XfKyRDVN7AGZFNr3A _model_server_result.datetime_utc '2024-10-25 20:26:18' _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 6rvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":502}' # _entry.id 6RVB # _exptl.entry_id 6RVB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 4 _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 6RVB _cell.length_a 160.75 _cell.length_b 160.75 _cell.length_c 256.92 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # 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 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,Q,R 1 1 C,K,L,M,S 2 1 D,N,O,P,T 2 2 # 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' 2_645 -x+1,-y-1,z -1 0 0 0 -1 0 0 0 1 160.75 -160.75 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I N N ? 3 L N N ? 3 O 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 covale ? covale1 A SG CYS 44 A CYS 44 1_555 G S1P COA . A COA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? covale ? covale2 B SG CYS 44 B CYS 44 1_555 J S1P COA . B COA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? covale ? covale3 C SG CYS 44 C CYS 44 1_555 M S1P COA . C COA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? covale ? covale4 D SG CYS 44 D CYS 44 1_555 P S1P COA . D COA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 PA O1A NAD doub 414 n n PA O2A NAD sing 415 n n PA O5B NAD sing 416 n n PA O3 NAD sing 417 n n O2A HOA2 NAD sing 418 n n O5B C5B NAD sing 419 n n C5B C4B NAD sing 420 n n C5B H51A NAD sing 421 n n C5B H52A NAD sing 422 n n C4B O4B NAD sing 423 n n C4B C3B NAD sing 424 n n C4B H4B NAD sing 425 n n O4B C1B NAD sing 426 n n C3B O3B NAD sing 427 n n C3B C2B NAD sing 428 n n C3B H3B NAD sing 429 n n O3B HO3A NAD sing 430 n n C2B O2B NAD sing 431 n n C2B C1B NAD sing 432 n n C2B H2B NAD sing 433 n n O2B HO2A NAD sing 434 n n C1B N9A NAD sing 435 n n C1B H1B NAD sing 436 n n N9A C8A NAD sing 437 n y N9A C4A NAD sing 438 n y C8A N7A NAD doub 439 n y C8A H8A NAD sing 440 n n N7A C5A NAD sing 441 n y C5A C6A NAD sing 442 n y C5A C4A NAD doub 443 n y C6A N6A NAD sing 444 n n C6A N1A NAD doub 445 n y N6A H61A NAD sing 446 n n N6A H62A NAD sing 447 n n N1A C2A NAD sing 448 n y C2A N3A NAD doub 449 n y C2A H2A NAD sing 450 n n N3A C4A NAD sing 451 n y O3 PN NAD sing 452 n n PN O1N NAD doub 453 n n PN O2N NAD sing 454 n n PN O5D NAD sing 455 n n O5D C5D NAD sing 456 n n C5D C4D NAD sing 457 n n C5D H51N NAD sing 458 n n C5D H52N NAD sing 459 n n C4D O4D NAD sing 460 n n C4D C3D NAD sing 461 n n C4D H4D NAD sing 462 n n O4D C1D NAD sing 463 n n C3D O3D NAD sing 464 n n C3D C2D NAD sing 465 n n C3D H3D NAD sing 466 n n O3D HO3N NAD sing 467 n n C2D O2D NAD sing 468 n n C2D C1D NAD sing 469 n n C2D H2D NAD sing 470 n n O2D HO2N NAD sing 471 n n C1D N1N NAD sing 472 n n C1D H1D NAD sing 473 n n N1N C2N NAD sing 474 n y N1N C6N NAD doub 475 n y C2N C3N NAD doub 476 n y C2N H2N NAD sing 477 n n C3N C7N NAD sing 478 n n C3N C4N NAD sing 479 n y C7N O7N NAD doub 480 n n C7N N7N NAD sing 481 n n N7N H71N NAD sing 482 n n N7N H72N NAD sing 483 n n C4N C5N NAD doub 484 n y C4N H4N NAD sing 485 n n C5N C6N NAD sing 486 n y C5N H5N NAD sing 487 n n C6N H6N NAD sing 488 n n # _atom_sites.entry_id 6RVB _atom_sites.fract_transf_matrix[1][1] 0.006221 _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] 0.006221 _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] 0.003892 _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 FAD A 1 501 501 FAD FAD . F 3 NAD A 1 502 502 NAD NAD . G 4 COA A 1 503 503 COA COA . H 2 FAD B 1 501 501 FAD FAD . I 3 NAD B 1 502 502 NAD NAD . J 4 COA B 1 503 503 COA COA . K 2 FAD C 1 501 501 FAD FAD . L 3 NAD C 1 502 502 NAD NAD . M 4 COA C 1 503 503 COA COA . N 2 FAD D 1 501 501 FAD FAD . O 3 NAD D 1 502 502 NAD NAD . P 4 COA D 1 503 503 COA COA . Q 5 HOH A 1 601 112 HOH HOH . Q 5 HOH A 2 602 91 HOH HOH . Q 5 HOH A 3 603 52 HOH HOH . Q 5 HOH A 4 604 15 HOH HOH . Q 5 HOH A 5 605 12 HOH HOH . Q 5 HOH A 6 606 106 HOH HOH . Q 5 HOH A 7 607 40 HOH HOH . Q 5 HOH A 8 608 18 HOH HOH . Q 5 HOH A 9 609 5 HOH HOH . Q 5 HOH A 10 610 75 HOH HOH . Q 5 HOH A 11 611 54 HOH HOH . Q 5 HOH A 12 612 33 HOH HOH . Q 5 HOH A 13 613 2 HOH HOH . Q 5 HOH A 14 614 20 HOH HOH . Q 5 HOH A 15 615 68 HOH HOH . Q 5 HOH A 16 616 47 HOH HOH . Q 5 HOH A 17 617 39 HOH HOH . Q 5 HOH A 18 618 62 HOH HOH . Q 5 HOH A 19 619 22 HOH HOH . Q 5 HOH A 20 620 103 HOH HOH . Q 5 HOH A 21 621 95 HOH HOH . Q 5 HOH A 22 622 41 HOH HOH . Q 5 HOH A 23 623 76 HOH HOH . Q 5 HOH A 24 624 35 HOH HOH . Q 5 HOH A 25 625 42 HOH HOH . Q 5 HOH A 26 626 30 HOH HOH . Q 5 HOH A 27 627 86 HOH HOH . Q 5 HOH A 28 628 105 HOH HOH . Q 5 HOH A 29 629 3 HOH HOH . Q 5 HOH A 30 630 96 HOH HOH . Q 5 HOH A 31 631 45 HOH HOH . Q 5 HOH A 32 632 58 HOH HOH . R 5 HOH B 1 601 34 HOH HOH . R 5 HOH B 2 602 70 HOH HOH . R 5 HOH B 3 603 37 HOH HOH . R 5 HOH B 4 604 51 HOH HOH . R 5 HOH B 5 605 48 HOH HOH . R 5 HOH B 6 606 82 HOH HOH . R 5 HOH B 7 607 104 HOH HOH . R 5 HOH B 8 608 85 HOH HOH . R 5 HOH B 9 609 88 HOH HOH . R 5 HOH B 10 610 26 HOH HOH . R 5 HOH B 11 611 100 HOH HOH . R 5 HOH B 12 612 77 HOH HOH . R 5 HOH B 13 613 93 HOH HOH . R 5 HOH B 14 614 32 HOH HOH . R 5 HOH B 15 615 16 HOH HOH . R 5 HOH B 16 616 99 HOH HOH . R 5 HOH B 17 617 74 HOH HOH . R 5 HOH B 18 618 63 HOH HOH . R 5 HOH B 19 619 4 HOH HOH . R 5 HOH B 20 620 24 HOH HOH . R 5 HOH B 21 621 60 HOH HOH . R 5 HOH B 22 622 46 HOH HOH . R 5 HOH B 23 623 55 HOH HOH . R 5 HOH B 24 624 9 HOH HOH . R 5 HOH B 25 625 111 HOH HOH . R 5 HOH B 26 626 102 HOH HOH . R 5 HOH B 27 627 109 HOH HOH . S 5 HOH C 1 601 1 HOH HOH . S 5 HOH C 2 602 13 HOH HOH . S 5 HOH C 3 603 17 HOH HOH . S 5 HOH C 4 604 21 HOH HOH . S 5 HOH C 5 605 89 HOH HOH . S 5 HOH C 6 606 65 HOH HOH . S 5 HOH C 7 607 11 HOH HOH . S 5 HOH C 8 608 7 HOH HOH . S 5 HOH C 9 609 23 HOH HOH . S 5 HOH C 10 610 66 HOH HOH . S 5 HOH C 11 611 90 HOH HOH . S 5 HOH C 12 612 50 HOH HOH . S 5 HOH C 13 613 97 HOH HOH . S 5 HOH C 14 614 71 HOH HOH . S 5 HOH C 15 615 36 HOH HOH . S 5 HOH C 16 616 80 HOH HOH . S 5 HOH C 17 617 44 HOH HOH . S 5 HOH C 18 618 53 HOH HOH . S 5 HOH C 19 619 59 HOH HOH . S 5 HOH C 20 620 84 HOH HOH . S 5 HOH C 21 621 38 HOH HOH . S 5 HOH C 22 622 73 HOH HOH . S 5 HOH C 23 623 94 HOH HOH . S 5 HOH C 24 624 107 HOH HOH . S 5 HOH C 25 625 61 HOH HOH . S 5 HOH C 26 626 110 HOH HOH . S 5 HOH C 27 627 98 HOH HOH . T 5 HOH D 1 601 27 HOH HOH . T 5 HOH D 2 602 83 HOH HOH . T 5 HOH D 3 603 108 HOH HOH . T 5 HOH D 4 604 78 HOH HOH . T 5 HOH D 5 605 31 HOH HOH . T 5 HOH D 6 606 64 HOH HOH . T 5 HOH D 7 607 28 HOH HOH . T 5 HOH D 8 608 56 HOH HOH . T 5 HOH D 9 609 14 HOH HOH . T 5 HOH D 10 610 92 HOH HOH . T 5 HOH D 11 611 25 HOH HOH . T 5 HOH D 12 612 10 HOH HOH . T 5 HOH D 13 613 67 HOH HOH . T 5 HOH D 14 614 6 HOH HOH . T 5 HOH D 15 615 43 HOH HOH . T 5 HOH D 16 616 19 HOH HOH . T 5 HOH D 17 617 8 HOH HOH . T 5 HOH D 18 618 69 HOH HOH . T 5 HOH D 19 619 49 HOH HOH . T 5 HOH D 20 620 29 HOH HOH . T 5 HOH D 21 621 87 HOH HOH . T 5 HOH D 22 622 72 HOH HOH . T 5 HOH D 23 623 101 HOH HOH . T 5 HOH D 24 624 57 HOH HOH . T 5 HOH D 25 625 79 HOH HOH . T 5 HOH D 26 626 81 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 P PA NAD . . . O 3 33.307 -48.302 28.005 1 45.71 ? PA NAD 502 D 1 HETATM 2 O O1A NAD . . . O 3 33.586 -49.755 28.038 1 48.24 ? O1A NAD 502 D 1 HETATM 3 O O2A NAD . . . O 3 31.903 -47.808 28.112 1 50.74 ? O2A NAD 502 D 1 HETATM 4 O O5B NAD . . . O 3 34.15 -47.623 29.247 1 74.39 ? O5B NAD 502 D 1 HETATM 5 C C5B NAD . . . O 3 33.836 -47.549 30.687 1 77.89 ? C5B NAD 502 D 1 HETATM 6 C C4B NAD . . . O 3 33.833 -46.063 31.211 1 59.28 ? C4B NAD 502 D 1 HETATM 7 O O4B NAD . . . O 3 33.773 -45.42 32.533 1 45.34 ? O4B NAD 502 D 1 HETATM 8 C C3B NAD . . . O 3 35.095 -45.521 30.622 1 52.9 ? C3B NAD 502 D 1 HETATM 9 O O3B NAD . . . O 3 34.938 -45.716 29.234 1 56.1 ? O3B NAD 502 D 1 HETATM 10 C C2B NAD . . . O 3 34.918 -44.092 31.067 1 55.96 ? C2B NAD 502 D 1 HETATM 11 O O2B NAD . . . O 3 34.394 -43.071 30.214 1 62.6 ? O2B NAD 502 D 1 HETATM 12 C C1B NAD . . . O 3 33.801 -44.036 32.047 1 50 ? C1B NAD 502 D 1 HETATM 13 N N9A NAD . . . O 3 34.645 -42.803 32.362 1 72.2 ? N9A NAD 502 D 1 HETATM 14 C C8A NAD . . . O 3 35.923 -42.599 33.008 1 78.18 ? C8A NAD 502 D 1 HETATM 15 N N7A NAD . . . O 3 36.437 -41.296 33.045 1 56.22 ? N7A NAD 502 D 1 HETATM 16 C C5A NAD . . . O 3 35.472 -40.672 32.36 1 49.09 ? C5A NAD 502 D 1 HETATM 17 C C6A NAD . . . O 3 35.493 -39.404 32.089 1 47.27 ? C6A NAD 502 D 1 HETATM 18 N N6A NAD . . . O 3 36.566 -38.843 32.554 1 53.05 ? N6A NAD 502 D 1 HETATM 19 N N1A NAD . . . O 3 34.497 -38.826 31.338 1 64.41 ? N1A NAD 502 D 1 HETATM 20 C C2A NAD . . . O 3 33.475 -39.674 30.878 1 78.61 ? C2A NAD 502 D 1 HETATM 21 N N3A NAD . . . O 3 33.443 -41.055 31.144 1 48.09 ? N3A NAD 502 D 1 HETATM 22 C C4A NAD . . . O 3 34.424 -41.521 31.901 1 53.29 ? C4A NAD 502 D 1 HETATM 23 O O3 NAD . . . O 3 33.814 -47.782 26.601 1 48.1 ? O3 NAD 502 D 1 HETATM 24 P PN NAD . . . O 3 35.061 -48.266 25.718 1 55.61 ? PN NAD 502 D 1 HETATM 25 O O1N NAD . . . O 3 35.29 -47.009 24.888 1 48.43 ? O1N NAD 502 D 1 HETATM 26 O O2N NAD . . . O 3 36.218 -48.819 26.4 1 55.75 ? O2N NAD 502 D 1 HETATM 27 O O5D NAD . . . O 3 34.487 -49.596 25.066 1 47.18 ? O5D NAD 502 D 1 HETATM 28 C C5D NAD . . . O 3 34.709 -49.823 23.672 1 65.32 ? C5D NAD 502 D 1 HETATM 29 C C4D NAD . . . O 3 33.781 -50.861 23.042 1 58.34 ? C4D NAD 502 D 1 HETATM 30 O O4D NAD . . . O 3 34.295 -51.458 21.83 1 62.17 ? O4D NAD 502 D 1 HETATM 31 C C3D NAD . . . O 3 33.525 -51.924 24.114 1 69.72 ? C3D NAD 502 D 1 HETATM 32 O O3D NAD . . . O 3 32.449 -51.65 25.046 1 73 ? O3D NAD 502 D 1 HETATM 33 C C2D NAD . . . O 3 33.331 -53.128 23.224 1 71.55 ? C2D NAD 502 D 1 HETATM 34 O O2D NAD . . . O 3 31.981 -53.176 22.85 1 79.87 ? O2D NAD 502 D 1 HETATM 35 C C1D NAD . . . O 3 34.223 -52.854 22.019 1 63.1 ? C1D NAD 502 D 1 HETATM 36 N N1N NAD . . . O 3 35.467 -53.418 22.544 1 70.17 ? N1N NAD 502 D 1 HETATM 37 C C2N NAD . . . O 3 35.485 -54.722 23.024 1 82.13 ? C2N NAD 502 D 1 HETATM 38 C C3N NAD . . . O 3 36.637 -55.338 23.586 1 82.72 ? C3N NAD 502 D 1 HETATM 39 C C7N NAD . . . O 3 36.647 -56.779 24.033 1 76.89 ? C7N NAD 502 D 1 HETATM 40 O O7N NAD . . . O 3 35.388 -57.439 24.208 1 70.24 ? O7N NAD 502 D 1 HETATM 41 N N7N NAD . . . O 3 37.859 -57.365 24.199 1 69.72 ? N7N NAD 502 D 1 HETATM 42 C C4N NAD . . . O 3 37.816 -54.603 23.672 1 79.13 ? C4N NAD 502 D 1 HETATM 43 C C5N NAD . . . O 3 37.782 -53.271 23.215 1 82.26 ? C5N NAD 502 D 1 HETATM 44 C C6N NAD . . . O 3 36.609 -52.683 22.666 1 78.88 ? C6N NAD 502 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #