SMTL ID : 5aga.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 12 residues within 4Å: Chain A: V.25, K.27, Q.32, T.53, S.54, A.55, G.56, K.57, T.58, L.59, N.387 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.27, A:Q.32, A:T.53, A:S.54, A:A.55, A:G.56, A:K.57, A:K.57, A:T.58, A:T.58, A:N.387 pi-Stacking: A:F.29 ANP.5: 12 residues within 4Å: Chain B: V.25, K.27, Q.32, T.53, S.54, A.55, G.56, K.57, T.58, L.59, N.387 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.27, B:Q.32, B:T.53, B:S.54, B:A.55, B:G.56, B:K.57, B:K.57, B:T.58, B:T.58, B:N.387 pi-Stacking: B:F.29 ANP.9: 12 residues within 4Å: Chain C: V.25, K.27, Q.32, T.53, S.54, A.55, G.56, K.57, T.58, L.59, N.387 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.27, C:Q.32, C:T.53, C:T.53, C:S.54, C:A.55, C:G.56, C:K.57, C:K.57, C:T.58, C:T.58, C:N.387 pi-Stacking: C:F.29 ANP.13: 12 residues within 4Å: Chain D: V.25, K.27, Q.32, T.53, S.54, A.55, G.56, K.57, T.58, L.59, N.387 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.27, D:Q.32, D:T.53, D:T.53, D:S.54, D:A.55, D:G.56, D:K.57, D:K.57, D:T.58, D:T.58, D:N.387 pi-Stacking: D:F.29

4 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 5 residues within 4Å: Chain A: I.270, I.317, P.346, W.347, G.348 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.317 Salt bridges: A:H.301 FLC.6: 5 residues within 4Å: Chain B: I.270, I.317, P.346, W.347, G.348 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.317 Salt bridges: B:H.301 FLC.10: 5 residues within 4Å: Chain C: I.270, I.317, P.346, W.347, G.348 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.317 Salt bridges: C:H.301 FLC.14: 5 residues within 4Å: Chain D: I.270, I.317, P.346, W.347, G.348 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.317 Salt bridges: D:H.301

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: F.723, V.733, V.735, S.736, L.738 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.735, A:S.736, A:L.738 K.7: 5 residues within 4Å: Chain B: F.723, V.733, V.735, S.736, L.738 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.735, B:S.736, B:L.738 K.11: 5 residues within 4Å: Chain C: F.723, V.733, V.735, S.736, L.738 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:V.735, C:S.736, C:L.738 K.15: 5 residues within 4Å: Chain D: F.723, V.733, V.735, S.736, L.738 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:V.735, D:S.736, D:L.738

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.57, D.152 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: K.57, D.152 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: K.57, D.152 Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: K.57, D.152 Ligands: ANP.13 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

2015-02-25

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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