SMTL ID : 1xsl.4 (3 other biounits)

Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x DG- DT- DG- DC- DG- DC: 5'-D(*GP*TP*GP*CP*GP*C)-3'(Non-covalent)

DG-DT-DG-DC-DG-DC.1: 21 residues within 4Å: Chain A: A.5, G.6, C.7, G.8, C.9, A.10, C.11 Chain B: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, K.232, L.234, R.248, Y.265, F.266 Ligands: NA.4 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:W.34 Hydrogen bonds: B:T.131, B:T.131, B:T.131, B:E.226, B:Y.265, B:Y.265, B:Y.265 Water bridges: B:W.34, B:Q.132, B:E.225, B:E.225, B:E.226, B:E.226, B:N.227, B:R.277, B:R.277, B:R.277, B:R.277, B:K.281 Salt bridges: B:R.277, B:K.281 pi-Stacking: B:W.34 pi-Cation interactions: B:R.277, B:R.277

1 x DG- DC- DC- DG: 5'-D(P*GP*CP*CP*G)-3'(Non-covalent)

DG-DC-DC-DG.2: 19 residues within 4Å: Chain A: C.1, G.2, G.3, C.4 Chain B: Y.27, W.34, R.35, G.38, Y.39, I.62, P.63, G.64, I.65, G.66, K.67, R.68, M.69, K.72, K.84 Protein-ligand interaction information (PLIP) not available

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 5 residues within 4Å: Chain B: S.99, I.101, G.103, A.104 Ligands: DG-DT-DG-DC-DG-DC.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.99, B:G.103, B:A.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., A closed conformation for the Pol lambda catalytic cycle. Nat.Struct.Mol.Biol. (2005)

Release Date

2005-01-18

Peptides

DNA polymerase lambda: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
M

DNA polymerase lambda

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