SMTL ID : 4k4g.4 (3 other biounits)

Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC.1: 23 residues within 4Å: Chain A: I.98, W.99, G.100, A.101, G.102, T.103, K.104, T.105, K.229, L.231, R.245, D.247, Y.262, F.263 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: 1S0.4, CA.7 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.2: 20 residues within 4Å: Chain A: Y.24, W.31, R.32, G.35, Y.36, I.59, P.60, G.61, I.62, G.63, K.64, R.65, M.66, K.69, K.81 Chain B: C.1, G.2, G.3, C.4 Ligands: CA.6 Protein-ligand interaction information (PLIP) not available

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: E.223 Chain B: A.8, C.9 No protein-ligand interaction detected (PLIP)

1 x 1S0: 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

1S0.4: 16 residues within 4Å: Chain A: R.143, G.173, S.174, R.177, C.182, G.183, D.184, Y.262, F.263, S.266, A.267, N.270, R.274 Chain B: G.5 Ligands: DC-DA-DG-DT-DA-DC.1, CA.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.262 Hydrogen bonds: A:S.174, A:S.174, A:G.183, A:F.263, A:A.267, A:N.270, A:R.274, A:R.274 Water bridges: A:S.174, A:D.184, A:D.184, A:D.184 Salt bridges: A:R.143, A:R.177

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.184, D.186 Ligands: 1S0.4, CA.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, A:D.186, H2O.4, H2O.4 CA.6: 5 residues within 4Å: Chain A: C.57, I.59, P.60, I.62 Ligands: DG-DC-DC-DG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.57, A:I.59, A:I.62 CA.7: 4 residues within 4Å: Chain A: S.96, I.98, A.101 Ligands: DC-DA-DG-DT-DA-DC.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.96, A:I.98, A:A.101, H2O.5 CA.8: 4 residues within 4Å: Chain A: D.184, D.186, D.247 Ligands: CA.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, A:D.186, A:D.247, H2O.3, H2O.4

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.9: 1 residues within 4Å: Chain A: E.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-16

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

DNA polymerase lambda

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