SMTL ID : 5aho.1

Crystal structure of human 5' exonuclease Apollo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 8 residues within 4Å: Chain A: N.177, K.179, E.225, H.231, W.246, T.249, H.250, T.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.177, A:K.179, A:E.225, A:T.252 EDO.2: 5 residues within 4Å: Chain A: L.134, G.137, K.138, I.140, L.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.290 Water bridges: A:L.134, A:L.136, A:G.137 EDO.3: 7 residues within 4Å: Chain A: S.52, I.54, V.75, D.97, G.103, S.104, V.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.103 Water bridges: A:S.52 EDO.4: 4 residues within 4Å: Chain A: T.90, M.91, T.92, E.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.90, A:T.92 Water bridges: A:T.90 EDO.5: 3 residues within 4Å: Chain A: G.40, S.42, T.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.42, A:T.44 EDO.10: 8 residues within 4Å: Chain A: G.181, L.182, Y.183, K.187, H.235, L.256, P.257 Ligands: TLA.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.187, A:K.187

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.6: 11 residues within 4Å: Chain A: H.32, H.34, D.36, H.37, H.100, D.121, Y.183, H.277 Ligands: ZN.7, ZN.8, TLA.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.3 Water bridges: A:D.36, A:D.36 Salt bridges: A:H.34, A:H.100, A:H.277, A:H.277 TLA.9: 11 residues within 4Å: Chain A: Y.183, K.187, T.258, S.259, R.260, Y.274, S.275, D.276, H.277 Ligands: TLA.6, EDO.10 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.187, A:T.258, A:T.258, A:T.258, A:S.259, A:D.276 Water bridges: A:R.260, A:R.260 Salt bridges: A:K.187, A:R.260, A:H.277

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: N.3, D.36, H.37, D.121 Ligands: TLA.6, ZN.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.36, A:H.37, A:D.121, H2O.1 ZN.8: 6 residues within 4Å: Chain A: H.32, H.34, H.100, D.121 Ligands: TLA.6, ZN.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.32, A:H.34, A:H.100, A:D.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allerston, C.K. et al., The Structures of the Snm1A and Snm1B/Apollo Nuclease Domains Reveal a Potential Basis for Their Distinct DNA Processing Activities. Nucleic Acids Res. (2015)

Release Date

2015-02-18

Peptides

5' EXONUCLEASE APOLLO: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

5' EXONUCLEASE APOLLO