SMTL ID : 5a9f.1

Crystal structure of the Helicase domain of human DNA polymerase theta in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: K.27, M.28, F.29, Q.32, P.52, T.53, S.54, A.55, G.56, K.57, T.58, L.59 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.32, A:Q.32, A:S.54, A:A.55, A:G.56, A:K.57, A:T.58, A:T.58 Salt bridges: A:K.57 ADP.4: 13 residues within 4Å: Chain B: K.27, M.28, F.29, Q.32, P.52, T.53, S.54, A.55, G.56, K.57, T.58, L.59 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.32, B:Q.32, B:S.54, B:A.55, B:G.56, B:K.57, B:T.58, B:T.58 Salt bridges: B:K.57 ADP.7: 13 residues within 4Å: Chain C: K.27, M.28, F.29, Q.32, P.52, T.53, S.54, A.55, G.56, K.57, T.58, L.59 Ligands: MG.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.32, C:Q.32, C:S.54, C:A.55, C:G.56, C:K.57, C:T.58 Salt bridges: C:K.57 ADP.10: 13 residues within 4Å: Chain D: K.27, M.28, F.29, Q.32, P.52, T.53, S.54, A.55, G.56, K.57, T.58, L.59 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.32, D:Q.32, D:S.54, D:A.55, D:G.56, D:K.57, D:T.58 Salt bridges: D:K.57

4 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: F.723, V.733, V.735, S.736, L.738 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.735, A:L.738 K.5: 5 residues within 4Å: Chain B: F.723, V.733, V.735, S.736, L.738 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.735, B:L.738 K.8: 5 residues within 4Å: Chain C: F.723, V.733, V.735, S.736, L.738 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:V.735, C:L.738 K.11: 5 residues within 4Å: Chain D: F.723, V.733, V.735, S.736, L.738 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:V.735, D:L.738

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.152 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.152 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: D.152 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain D: D.152 Ligands: ADP.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newman, J.A. et al., Structure of the Helicase Domain of DNA Polymerase Theta Reveals a Possible Role in the Microhomology-Mediated End-Joining Pathway. Structure (2015)

Release Date

2015-12-16

Peptides

DNA POLYMERASE THETA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

DNA POLYMERASE THETA

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