SMTL ID : 3cmt.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

1 x DG- DG- DT- DG- DG- DG: DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')(Non-covalent)

DG-DG-DT-DG-DG-DG.1: 15 residues within 4Å: Chain A: C.6, C.7, C.8, A.9, C.10, C.11 Chain B: G.175, S.486, M.488, I.523, S.835, M.837, R.842, M.1187, R.1192 Protein-ligand interaction information (PLIP) not available

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: T.48, E.71, D.119 Ligands: ALF.3, ADP.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.48, B:E.71 MG.4: 6 residues within 4Å: Chain B: T.397, E.420, D.468, K.923 Ligands: ALF.5, ADP.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.397, B:E.420 MG.6: 5 residues within 4Å: Chain B: T.746, E.769, D.817 Ligands: ALF.7, ADP.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.746 MG.8: 6 residues within 4Å: Chain B: T.1096, E.1119, D.1167, K.1622 Ligands: ALF.9, ADP.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.1096, B:E.1119 MG.10: 5 residues within 4Å: Chain B: T.1445, E.1468, D.1516 Ligands: ALF.11, ADP.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.1445

5 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 10 residues within 4Å: Chain B: E.43, S.44, K.47, T.48, E.71, F.541, K.572, K.574 Ligands: MG.2, ADP.12 No protein-ligand interaction detected (PLIP) ALF.5: 10 residues within 4Å: Chain B: E.392, S.393, K.396, T.397, E.420, F.890, K.921, K.923 Ligands: MG.4, ADP.13 No protein-ligand interaction detected (PLIP) ALF.7: 10 residues within 4Å: Chain B: E.741, S.742, K.745, T.746, E.769, F.1240, K.1271, K.1273 Ligands: MG.6, ADP.14 No protein-ligand interaction detected (PLIP) ALF.9: 10 residues within 4Å: Chain B: E.1091, S.1092, K.1095, T.1096, E.1119, F.1589, K.1620, K.1622 Ligands: MG.8, ADP.15 No protein-ligand interaction detected (PLIP) ALF.11: 7 residues within 4Å: Chain B: E.1440, S.1441, K.1444, T.1445, E.1468 Ligands: MG.10, ADP.16 No protein-ligand interaction detected (PLIP)

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

ADP.12: 18 residues within 4Å: Chain B: S.44, S.45, G.46, K.47, T.48, T.49, D.75, Y.78, S.215, Y.239, N.573, K.574, I.575, A.576, A.577, P.578 Ligands: MG.2, ALF.3 15 PLIP interactions: 15 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.48, B:T.49, B:T.49, B:D.75, B:D.75, B:S.215 Salt bridges: B:K.47 pi-Stacking: B:Y.78, B:Y.78 ADP.13: 18 residues within 4Å: Chain B: S.393, S.394, G.395, K.396, T.397, T.398, D.424, Y.427, S.564, Y.588, N.922, K.923, I.924, A.925, A.926, P.927 Ligands: MG.4, ALF.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.393, B:S.394, B:G.395, B:K.396, B:T.397, B:T.397, B:T.398, B:T.398, B:D.424, B:S.564, B:S.564, B:I.924 Salt bridges: B:K.396 pi-Stacking: B:Y.427, B:Y.427 ADP.14: 18 residues within 4Å: Chain B: S.742, S.743, G.744, K.745, T.746, T.747, D.773, Y.776, S.913, Y.937, N.1272, K.1273, I.1274, A.1275, A.1276, P.1277 Ligands: MG.6, ALF.7 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.746, B:T.747, B:T.747, B:D.773, B:D.773, B:S.913, B:S.913 Salt bridges: B:K.745 pi-Stacking: B:Y.776, B:Y.776 ADP.15: 19 residues within 4Å: Chain B: E.1091, S.1092, S.1093, G.1094, K.1095, T.1096, T.1097, D.1123, Y.1126, S.1263, Y.1287, N.1621, K.1622, I.1623, A.1624, A.1625, P.1626 Ligands: MG.8, ALF.9 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.1092, B:S.1093, B:G.1094, B:K.1095, B:T.1096, B:T.1096, B:T.1097, B:T.1097, B:S.1263, B:S.1263, B:Y.1287, B:K.1622 Salt bridges: B:K.1095 pi-Stacking: B:Y.1126, B:Y.1126 ADP.16: 13 residues within 4Å: Chain B: E.1440, S.1441, S.1442, G.1443, K.1444, T.1445, T.1446, D.1472, Y.1475, S.1612, Y.1636 Ligands: MG.10, ALF.11 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.1441, B:S.1442, B:G.1443, B:K.1444, B:T.1445, B:T.1445, B:T.1446, B:D.1472, B:S.1612, B:S.1612, B:Y.1636 Salt bridges: B:K.1444 pi-Stacking: B:Y.1475, B:Y.1475

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

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