data_3NUT # _model_server_result.job_id XV083rIhO0ic1hF11323Kw _model_server_result.datetime_utc '2024-11-05 00:33:40' _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 3nut # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1501}' # _entry.id 3NUT # _exptl.entry_id 3NUT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 3NUT _cell.length_a 85.64 _cell.length_b 110.99 _cell.length_c 116.19 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NUT _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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,D,E,F,G,H,P,Q,T 1 1 B,C,I,J,K,L,M,N,O,R,S 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 E N N ? 2 I N N ? 2 M N N ? 2 P N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 290 n n N HN1 SAH sing 291 n n N HN2 SAH sing 292 n n CA CB SAH sing 293 n n CA C SAH sing 294 n n CA HA SAH sing 295 n n CB CG SAH sing 296 n n CB HB1 SAH sing 297 n n CB HB2 SAH sing 298 n n CG SD SAH sing 299 n n CG HG1 SAH sing 300 n n CG HG2 SAH sing 301 n n SD C5' SAH sing 302 n n C O SAH doub 303 n n C OXT SAH sing 304 n n OXT HXT SAH sing 305 n n C5' C4' SAH sing 306 n n C5' "H5'1" SAH sing 307 n n C5' "H5'2" SAH sing 308 n n C4' O4' SAH sing 309 n n C4' C3' SAH sing 310 n n C4' H4' SAH sing 311 n n O4' C1' SAH sing 312 n n C3' O3' SAH sing 313 n n C3' C2' SAH sing 314 n n C3' H3' SAH sing 315 n n O3' HO3' SAH sing 316 n n C2' O2' SAH sing 317 n n C2' C1' SAH sing 318 n n C2' H2' SAH sing 319 n n O2' HO2' SAH sing 320 n n C1' N9 SAH sing 321 n n C1' H1' SAH sing 322 n n N9 C8 SAH sing 323 n y N9 C4 SAH sing 324 n y C8 N7 SAH doub 325 n y C8 H8 SAH sing 326 n n N7 C5 SAH sing 327 n y C5 C6 SAH sing 328 n y C5 C4 SAH doub 329 n y C6 N6 SAH sing 330 n n C6 N1 SAH doub 331 n y N6 HN61 SAH sing 332 n n N6 HN62 SAH sing 333 n n N1 C2 SAH sing 334 n y C2 N3 SAH doub 335 n y C2 H2 SAH sing 336 n n N3 C4 SAH sing 337 n y # _atom_sites.entry_id 3NUT _atom_sites.fract_transf_matrix[1][1] 0.011677 _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] 0.00901 _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] 0.008607 _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 SAH A 1 1501 1501 SAH SAH . F 3 GOL A 1 246 1 GOL GOL . G 3 GOL A 1 247 2 GOL GOL . H 3 GOL A 1 248 2 GOL GOL . I 2 SAH B 1 1501 1501 SAH SAH . J 3 GOL B 1 246 1 GOL GOL . K 3 GOL B 1 247 1 GOL GOL . L 3 GOL B 1 248 3 GOL GOL . M 2 SAH C 1 1501 1501 SAH SAH . N 3 GOL C 1 246 1 GOL GOL . O 3 GOL C 1 247 1 GOL GOL . P 2 SAH D 1 1501 1501 SAH SAH . Q 4 HOH A 1 1506 1506 HOH HOH . Q 4 HOH A 2 1507 9 HOH HOH . Q 4 HOH A 3 1508 10 HOH HOH . Q 4 HOH A 4 1509 18 HOH HOH . Q 4 HOH A 5 1510 113 HOH HOH . Q 4 HOH A 6 1511 197 HOH HOH . Q 4 HOH A 7 1512 1512 HOH HOH . Q 4 HOH A 8 1515 1515 HOH HOH . Q 4 HOH A 9 1519 1519 HOH HOH . Q 4 HOH A 10 1524 1524 HOH HOH . Q 4 HOH A 11 1528 1528 HOH HOH . Q 4 HOH A 12 1532 1532 HOH HOH . Q 4 HOH A 13 1535 1535 HOH HOH . Q 4 HOH A 14 1538 1538 HOH HOH . Q 4 HOH A 15 1541 1541 HOH HOH . Q 4 HOH A 16 1547 1547 HOH HOH . Q 4 HOH A 17 1551 1551 HOH HOH . Q 4 HOH A 18 1562 1562 HOH HOH . Q 4 HOH A 19 1575 1575 HOH HOH . Q 4 HOH A 20 1579 1579 HOH HOH . Q 4 HOH A 21 1581 1581 HOH HOH . Q 4 HOH A 22 1591 1591 HOH HOH . Q 4 HOH A 23 1593 1593 HOH HOH . Q 4 HOH A 24 1595 1595 HOH HOH . Q 4 HOH A 25 1596 1596 HOH HOH . Q 4 HOH A 26 1597 1597 HOH HOH . Q 4 HOH A 27 1598 1598 HOH HOH . Q 4 HOH A 28 1604 1604 HOH HOH . Q 4 HOH A 29 1613 1613 HOH HOH . Q 4 HOH A 30 1624 1624 HOH HOH . Q 4 HOH A 31 1626 1626 HOH HOH . Q 4 HOH A 32 1630 1630 HOH HOH . Q 4 HOH A 33 1637 1637 HOH HOH . Q 4 HOH A 34 1642 1642 HOH HOH . Q 4 HOH A 35 1654 1654 HOH HOH . Q 4 HOH A 36 1655 1655 HOH HOH . Q 4 HOH A 37 1657 1657 HOH HOH . Q 4 HOH A 38 1678 1678 HOH HOH . Q 4 HOH A 39 1679 1679 HOH HOH . Q 4 HOH A 40 1700 1700 HOH HOH . Q 4 HOH A 41 1701 1701 HOH HOH . Q 4 HOH A 42 1707 1707 HOH HOH . Q 4 HOH A 43 1713 1713 HOH HOH . Q 4 HOH A 44 1715 1715 HOH HOH . Q 4 HOH A 45 1718 1718 HOH HOH . Q 4 HOH A 46 1721 1721 HOH HOH . R 4 HOH B 1 1502 1502 HOH HOH . R 4 HOH B 2 1503 1503 HOH HOH . R 4 HOH B 3 1504 2 HOH HOH . R 4 HOH B 4 1505 1505 HOH HOH . R 4 HOH B 5 1506 24 HOH HOH . R 4 HOH B 6 1507 25 HOH HOH . R 4 HOH B 7 1508 47 HOH HOH . R 4 HOH B 8 1509 130 HOH HOH . R 4 HOH B 9 1513 1513 HOH HOH . R 4 HOH B 10 1518 1518 HOH HOH . R 4 HOH B 11 1529 1529 HOH HOH . R 4 HOH B 12 1531 1531 HOH HOH . R 4 HOH B 13 1534 1534 HOH HOH . R 4 HOH B 14 1543 1543 HOH HOH . R 4 HOH B 15 1544 1544 HOH HOH . R 4 HOH B 16 1545 1545 HOH HOH . R 4 HOH B 17 1555 1555 HOH HOH . R 4 HOH B 18 1558 1558 HOH HOH . R 4 HOH B 19 1561 1561 HOH HOH . R 4 HOH B 20 1563 1563 HOH HOH . R 4 HOH B 21 1570 1570 HOH HOH . R 4 HOH B 22 1571 1571 HOH HOH . R 4 HOH B 23 1572 1572 HOH HOH . R 4 HOH B 24 1577 1577 HOH HOH . R 4 HOH B 25 1580 1580 HOH HOH . R 4 HOH B 26 1585 1585 HOH HOH . R 4 HOH B 27 1589 1589 HOH HOH . R 4 HOH B 28 1592 1592 HOH HOH . R 4 HOH B 29 1600 1600 HOH HOH . R 4 HOH B 30 1603 1603 HOH HOH . R 4 HOH B 31 1612 1612 HOH HOH . R 4 HOH B 32 1621 1621 HOH HOH . R 4 HOH B 33 1622 1622 HOH HOH . R 4 HOH B 34 1625 1625 HOH HOH . R 4 HOH B 35 1628 1628 HOH HOH . R 4 HOH B 36 1629 1629 HOH HOH . R 4 HOH B 37 1631 1631 HOH HOH . R 4 HOH B 38 1632 1632 HOH HOH . R 4 HOH B 39 1635 1635 HOH HOH . R 4 HOH B 40 1638 1638 HOH HOH . R 4 HOH B 41 1644 1644 HOH HOH . R 4 HOH B 42 1652 1652 HOH HOH . R 4 HOH B 43 1660 1660 HOH HOH . R 4 HOH B 44 1661 1661 HOH HOH . R 4 HOH B 45 1673 1673 HOH HOH . R 4 HOH B 46 1675 1675 HOH HOH . R 4 HOH B 47 1676 1676 HOH HOH . R 4 HOH B 48 1684 1684 HOH HOH . R 4 HOH B 49 1688 1688 HOH HOH . R 4 HOH B 50 1689 1689 HOH HOH . R 4 HOH B 51 1696 1696 HOH HOH . R 4 HOH B 52 1699 1699 HOH HOH . R 4 HOH B 53 1705 1705 HOH HOH . R 4 HOH B 54 1706 1706 HOH HOH . S 4 HOH C 1 1507 1507 HOH HOH . S 4 HOH C 2 1508 1508 HOH HOH . S 4 HOH C 3 1509 4 HOH HOH . S 4 HOH C 4 1510 7 HOH HOH . S 4 HOH C 5 1511 19 HOH HOH . S 4 HOH C 6 1512 76 HOH HOH . S 4 HOH C 7 1513 94 HOH HOH . S 4 HOH C 8 1514 1514 HOH HOH . S 4 HOH C 9 1515 121 HOH HOH . S 4 HOH C 10 1516 123 HOH HOH . S 4 HOH C 11 1517 1517 HOH HOH . S 4 HOH C 12 1518 160 HOH HOH . S 4 HOH C 13 1519 175 HOH HOH . S 4 HOH C 14 1522 1522 HOH HOH . S 4 HOH C 15 1525 1525 HOH HOH . S 4 HOH C 16 1527 1527 HOH HOH . S 4 HOH C 17 1533 1533 HOH HOH . S 4 HOH C 18 1540 1540 HOH HOH . S 4 HOH C 19 1546 1546 HOH HOH . S 4 HOH C 20 1550 1550 HOH HOH . S 4 HOH C 21 1552 1552 HOH HOH . S 4 HOH C 22 1554 1554 HOH HOH . S 4 HOH C 23 1557 1557 HOH HOH . S 4 HOH C 24 1560 1560 HOH HOH . S 4 HOH C 25 1564 1564 HOH HOH . S 4 HOH C 26 1567 1567 HOH HOH . S 4 HOH C 27 1569 1569 HOH HOH . S 4 HOH C 28 1573 1573 HOH HOH . S 4 HOH C 29 1586 1586 HOH HOH . S 4 HOH C 30 1587 1587 HOH HOH . S 4 HOH C 31 1605 1605 HOH HOH . S 4 HOH C 32 1609 1609 HOH HOH . S 4 HOH C 33 1611 1611 HOH HOH . S 4 HOH C 34 1619 1619 HOH HOH . S 4 HOH C 35 1623 1623 HOH HOH . S 4 HOH C 36 1639 1639 HOH HOH . S 4 HOH C 37 1640 1640 HOH HOH . S 4 HOH C 38 1641 1641 HOH HOH . S 4 HOH C 39 1645 1645 HOH HOH . S 4 HOH C 40 1647 1647 HOH HOH . S 4 HOH C 41 1656 1656 HOH HOH . S 4 HOH C 42 1658 1658 HOH HOH . S 4 HOH C 43 1662 1662 HOH HOH . S 4 HOH C 44 1663 1663 HOH HOH . S 4 HOH C 45 1664 1664 HOH HOH . S 4 HOH C 46 1665 1665 HOH HOH . S 4 HOH C 47 1667 1667 HOH HOH . S 4 HOH C 48 1671 1671 HOH HOH . S 4 HOH C 49 1672 1672 HOH HOH . S 4 HOH C 50 1677 1677 HOH HOH . S 4 HOH C 51 1680 1680 HOH HOH . S 4 HOH C 52 1683 1683 HOH HOH . S 4 HOH C 53 1694 1694 HOH HOH . S 4 HOH C 54 1695 1695 HOH HOH . S 4 HOH C 55 1703 1703 HOH HOH . S 4 HOH C 56 1710 1710 HOH HOH . S 4 HOH C 57 1714 1714 HOH HOH . S 4 HOH C 58 1719 1719 HOH HOH . S 4 HOH C 59 1720 1720 HOH HOH . T 4 HOH D 1 1510 1510 HOH HOH . T 4 HOH D 2 1511 13 HOH HOH . T 4 HOH D 3 1512 20 HOH HOH . T 4 HOH D 4 1513 27 HOH HOH . T 4 HOH D 5 1514 89 HOH HOH . T 4 HOH D 6 1515 186 HOH HOH . T 4 HOH D 7 1521 1521 HOH HOH . T 4 HOH D 8 1523 1523 HOH HOH . T 4 HOH D 9 1526 1526 HOH HOH . T 4 HOH D 10 1536 1536 HOH HOH . T 4 HOH D 11 1537 1537 HOH HOH . T 4 HOH D 12 1549 1549 HOH HOH . T 4 HOH D 13 1553 1553 HOH HOH . T 4 HOH D 14 1556 1556 HOH HOH . T 4 HOH D 15 1565 1565 HOH HOH . T 4 HOH D 16 1566 1566 HOH HOH . T 4 HOH D 17 1568 1568 HOH HOH . T 4 HOH D 18 1574 1574 HOH HOH . T 4 HOH D 19 1576 1576 HOH HOH . T 4 HOH D 20 1578 1578 HOH HOH . T 4 HOH D 21 1582 1582 HOH HOH . T 4 HOH D 22 1584 1584 HOH HOH . T 4 HOH D 23 1601 1601 HOH HOH . T 4 HOH D 24 1602 1602 HOH HOH . T 4 HOH D 25 1608 1608 HOH HOH . T 4 HOH D 26 1614 1614 HOH HOH . T 4 HOH D 27 1616 1616 HOH HOH . T 4 HOH D 28 1617 1617 HOH HOH . T 4 HOH D 29 1618 1618 HOH HOH . T 4 HOH D 30 1634 1634 HOH HOH . T 4 HOH D 31 1651 1651 HOH HOH . T 4 HOH D 32 1666 1666 HOH HOH . T 4 HOH D 33 1668 1668 HOH HOH . T 4 HOH D 34 1670 1670 HOH HOH . T 4 HOH D 35 1685 1685 HOH HOH . T 4 HOH D 36 1716 1716 HOH HOH . T 4 HOH D 37 1722 1722 HOH HOH . T 4 HOH D 38 1723 1723 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 N N SAH . . . M 2 10.831 36.2 42.815 1 32.36 ? N SAH 1501 C 1 HETATM 2 C CA SAH . . . M 2 10.419 37.597 43.039 1 32.19 ? CA SAH 1501 C 1 HETATM 3 C CB SAH . . . M 2 9.723 37.658 44.384 1 33.49 ? CB SAH 1501 C 1 HETATM 4 C CG SAH . . . M 2 8.248 37.498 44.069 1 36.03 ? CG SAH 1501 C 1 HETATM 5 S SD SAH . . . M 2 7.375 37.317 45.572 1 43.07 ? SD SAH 1501 C 1 HETATM 6 C C SAH . . . M 2 11.632 38.459 43.074 1 32.32 ? C SAH 1501 C 1 HETATM 7 O O SAH . . . M 2 12.735 37.922 42.987 1 30.4 ? O SAH 1501 C 1 HETATM 8 O OXT SAH . . . M 2 11.531 39.713 43.212 1 31.96 ? OXT SAH 1501 C 1 HETATM 9 C C5' SAH . . . M 2 6.328 38.764 45.425 1 39.68 ? C5' SAH 1501 C 1 HETATM 10 C C4' SAH . . . M 2 6.859 40.013 46.157 1 38.08 ? C4' SAH 1501 C 1 HETATM 11 O O4' SAH . . . M 2 8.048 40.553 45.552 1 37.99 ? O4' SAH 1501 C 1 HETATM 12 C C3' SAH . . . M 2 5.909 41.221 46.26 1 38.87 ? C3' SAH 1501 C 1 HETATM 13 O O3' SAH . . . M 2 5.011 41.209 47.381 1 42.97 ? O3' SAH 1501 C 1 HETATM 14 C C2' SAH . . . M 2 6.842 42.41 46.495 1 38.19 ? C2' SAH 1501 C 1 HETATM 15 O O2' SAH . . . M 2 7.238 42.496 47.889 1 33.4 ? O2' SAH 1501 C 1 HETATM 16 C C1' SAH . . . M 2 8.043 42.015 45.64 1 35.56 ? C1' SAH 1501 C 1 HETATM 17 N N9 SAH . . . M 2 7.992 42.678 44.3 1 33.86 ? N9 SAH 1501 C 1 HETATM 18 C C8 SAH . . . M 2 7.924 42.059 43.102 1 32.49 ? C8 SAH 1501 C 1 HETATM 19 N N7 SAH . . . M 2 7.945 42.975 42.078 1 35.85 ? N7 SAH 1501 C 1 HETATM 20 C C5 SAH . . . M 2 8.024 44.214 42.611 1 33.4 ? C5 SAH 1501 C 1 HETATM 21 C C6 SAH . . . M 2 8.078 45.608 42.097 1 36.48 ? C6 SAH 1501 C 1 HETATM 22 N N6 SAH . . . M 2 8.045 45.9 40.758 1 36.02 ? N6 SAH 1501 C 1 HETATM 23 N N1 SAH . . . M 2 8.168 46.604 43.015 1 36.5 ? N1 SAH 1501 C 1 HETATM 24 C C2 SAH . . . M 2 8.2 46.361 44.346 1 36.02 ? C2 SAH 1501 C 1 HETATM 25 N N3 SAH . . . M 2 8.154 45.119 44.86 1 33.2 ? N3 SAH 1501 C 1 HETATM 26 C C4 SAH . . . M 2 8.056 44.017 44.067 1 34.38 ? C4 SAH 1501 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #