SMTL ID : 2r9l.1 (1 other biounit)

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DG-DC.1: 15 residues within 4Å: Chain A: G.1, C.2, C.3, G.4, C.5 Chain B: T.15, N.16, K.19, K.29, R.56, P.58, F.66, S.74, Q.107, Q.108 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.69, B:Q.70, B:T.91 Water bridges: B:F.67 pi-Stacking: B:F.66, B:F.67

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain B: L.186, E.188, L.198 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.188 EDO.3: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.289 EDO.4: 5 residues within 4Å: Chain B: H.114, Q.233, T.239, T.240, I.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.241 Water bridges: B:R.247 EDO.5: 6 residues within 4Å: Chain B: K.55, W.57, E.112, R.247, G.248, R.249 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.55, B:K.55, B:R.247, B:R.247, B:G.248

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain B: I.166, L.198, R.201 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.201, B:R.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brissett, N.C. et al., Structure of a NHEJ polymerase-mediated DNA synaptic complex. Science (2007)

Release Date

2008-01-08

Peptides

Putative DNA ligase-like protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Putative DNA ligase-like protein

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