SMTL ID : 3cmu.1

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

monomer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain B: T.48, E.71, D.119, K.574 Ligands: ALF.2, ADP.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.48, B:E.71 MG.3: 6 residues within 4Å: Chain B: T.397, E.420, D.468, K.923 Ligands: ALF.4, ADP.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.397 MG.5: 6 residues within 4Å: Chain B: T.746, E.769, D.817, K.1272 Ligands: ALF.6, ADP.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.746, B:E.769 MG.7: 6 residues within 4Å: Chain B: T.1095, E.1118, D.1166, K.1618 Ligands: ALF.8, ADP.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.1095 MG.9: 6 residues within 4Å: Chain B: T.1441, E.1464, D.1512, K.1966 Ligands: ALF.10, ADP.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.1441 MG.11: 5 residues within 4Å: Chain B: T.1789, E.1812, D.1860 Ligands: ALF.12, ADP.18 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.1789, B:E.1812

6 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 12 residues within 4Å: Chain B: E.43, S.44, K.47, T.48, E.71, D.119, S.120, F.541, K.572, K.574 Ligands: MG.1, ADP.13 No protein-ligand interaction detected (PLIP) ALF.4: 11 residues within 4Å: Chain B: E.392, S.393, K.396, T.397, E.420, D.468, F.890, K.921, K.923 Ligands: MG.3, ADP.14 No protein-ligand interaction detected (PLIP) ALF.6: 11 residues within 4Å: Chain B: E.741, S.742, K.745, T.746, E.769, D.817, F.1239, K.1270, K.1272 Ligands: MG.5, ADP.15 No protein-ligand interaction detected (PLIP) ALF.8: 11 residues within 4Å: Chain B: E.1090, S.1091, K.1094, T.1095, E.1118, D.1166, F.1585, K.1616, K.1618 Ligands: MG.7, ADP.16 No protein-ligand interaction detected (PLIP) ALF.10: 12 residues within 4Å: Chain B: E.1436, S.1437, K.1440, T.1441, E.1464, D.1512, S.1513, F.1933, K.1964, K.1966 Ligands: MG.9, ADP.17 No protein-ligand interaction detected (PLIP) ALF.12: 7 residues within 4Å: Chain B: E.1784, S.1785, K.1788, T.1789, E.1812 Ligands: MG.11, ADP.18 No protein-ligand interaction detected (PLIP)

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.13: 21 residues within 4Å: Chain B: P.42, E.43, S.44, S.45, G.46, K.47, T.48, T.49, D.75, Y.78, S.215, Y.239, K.572, N.573, K.574, I.575, A.576, A.577, P.578 Ligands: MG.1, ALF.2 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.44, B:S.44, B:S.45, B:G.46, B:K.47, B:T.48, B:T.49, B:T.49, B:S.215, B:S.215, B:N.573, B:K.574 Salt bridges: B:K.47, B:K.572, B:K.574 pi-Stacking: B:Y.78, B:Y.78 ADP.14: 21 residues within 4Å: Chain B: P.391, E.392, S.393, S.394, G.395, K.396, T.397, T.398, D.424, Y.427, S.564, Y.588, K.921, N.922, K.923, I.924, A.925, A.926, P.927 Ligands: MG.3, ALF.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.393, B:G.395, B:K.396, B:T.397, B:T.398, B:T.398, B:S.564, B:S.564, B:K.923 Salt bridges: B:K.396, B:K.921 pi-Stacking: B:Y.427, B:Y.427 ADP.15: 21 residues within 4Å: Chain B: P.740, E.741, S.742, S.743, G.744, K.745, T.746, T.747, D.773, Y.776, S.913, Y.937, K.1270, N.1271, K.1272, I.1273, A.1274, A.1275, P.1276 Ligands: MG.5, ALF.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.742, B:S.743, B:G.744, B:K.745, B:T.746, B:T.747, B:T.747, B:S.913, B:S.913, B:N.1271, B:K.1272 Salt bridges: B:K.745, B:K.1270, B:K.1272 pi-Stacking: B:Y.776 ADP.16: 21 residues within 4Å: Chain B: P.1089, E.1090, S.1091, S.1092, G.1093, K.1094, T.1095, T.1096, D.1122, Y.1125, S.1262, Y.1286, K.1616, N.1617, K.1618, I.1619, A.1620, A.1621, P.1622 Ligands: MG.7, ALF.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.1091, B:S.1091, B:S.1092, B:G.1093, B:K.1094, B:T.1095, B:T.1096, B:T.1096, B:S.1262, B:S.1262, B:N.1617, B:K.1618 Salt bridges: B:K.1094, B:K.1616 pi-Stacking: B:Y.1125, B:Y.1125 ADP.17: 20 residues within 4Å: Chain B: P.1435, E.1436, S.1437, S.1438, G.1439, K.1440, T.1441, T.1442, D.1468, Y.1471, S.1608, Y.1632, N.1965, K.1966, I.1967, A.1968, A.1969, P.1970 Ligands: MG.9, ALF.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.1437, B:G.1439, B:K.1440, B:T.1441, B:T.1442, B:T.1442, B:S.1608, B:S.1608, B:K.1966 Salt bridges: B:K.1440, B:K.1964 pi-Stacking: B:Y.1471, B:Y.1471 ADP.18: 14 residues within 4Å: Chain B: P.1783, E.1784, S.1785, S.1786, G.1787, K.1788, T.1789, T.1790, D.1816, Y.1819, S.1956, Y.1980 Ligands: MG.11, ALF.12 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:P.1783, B:S.1785, B:S.1786, B:G.1787, B:K.1788, B:T.1789, B:T.1789, B:T.1789, B:T.1790, B:T.1790, B:D.1816, B:S.1956, B:S.1956 Salt bridges: B:K.1788 pi-Stacking: B:Y.1819, B:Y.1819

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature (2008)

Release Date

2008-05-20

Peptides

Protein recA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Protein recA