SMTL ID : 3spl.2 (1 other biounit)

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.172, C.175, H.189, E.193 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.172, A:C.175, A:H.189, A:E.193 ZN.7: 4 residues within 4Å: Chain B: C.172, C.175, H.189, E.193 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.172, B:C.175, B:H.189, B:E.193

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 15 residues within 4Å: Chain A: L.10, Y.13, R.34, D.35, M.36, F.37, K.39, H.43, L.45, H.110, P.113, S.114, M.115, H.119, H.121 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.13, A:Y.13, A:M.36, A:F.37, A:K.39, A:K.39, A:S.114, A:M.115 Water bridges: A:N.9, A:N.9, A:N.9, A:H.110 Salt bridges: A:H.110, A:H.119, A:H.121 pi-Stacking: A:F.37 AMP.8: 14 residues within 4Å: Chain B: L.10, Y.13, D.35, M.36, F.37, K.39, H.43, L.45, H.110, P.113, S.114, M.115, H.119, H.121 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.13, B:Y.13, B:M.36, B:F.37, B:K.39, B:S.114, B:M.115 Water bridges: B:N.9, B:N.9, B:K.39, B:K.39, B:H.110, B:S.114 Salt bridges: B:H.110, B:H.119, B:H.121 pi-Stacking: B:F.37

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: L.53, H.65, R.66, S.67, L.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.67, A:L.68 Water bridges: A:R.66, A:S.67 Salt bridges: A:H.65 SO4.4: 3 residues within 4Å: Chain A: S.93, Q.94, Q.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.93, A:Q.94 SO4.5: 5 residues within 4Å: Chain A: H.57, A.111, G.112, R.159, G.160 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.160 Salt bridges: A:H.57, A:R.159 SO4.6: 2 residues within 4Å: Chain A: R.174, W.197 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.200, A:K.200 Salt bridges: A:R.174, A:K.200 SO4.9: 5 residues within 4Å: Chain B: L.53, H.65, R.66, S.67, L.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.67, B:L.68 Water bridges: B:R.66 Salt bridges: B:H.65 SO4.10: 3 residues within 4Å: Chain B: S.93, Q.94, Q.95 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.93, B:Q.94 SO4.11: 6 residues within 4Å: Chain B: H.57, A.111, G.112, P.113, R.159, G.160 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.160 Salt bridges: B:H.57, B:R.159 SO4.12: 3 residues within 4Å: Chain B: R.174, W.197, K.200 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.174, B:K.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, Y. et al., Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-10-12

Peptides

Aprataxin-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Aprataxin-like protein

Related Entries With Identical Sequence