SMTL ID : 2bgw.1

XPF from Aeropyrum pernix, complex with DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.42, E.52, R.53 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.42, A:E.52, A:R.53

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

SO4.2: 3 residues within 4Å: Chain A: P.5, R.135, R.139 No protein-ligand interaction detected (PLIP) SO4.3: 3 residues within 4Å: Chain A: S.20, P.21, R.53 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.53 SO4.4: 6 residues within 4Å: Chain A: P.39, M.40, G.41, Q.71, R.74, L.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.41, A:Q.71 Salt bridges: A:R.74 SO4.5: 3 residues within 4Å: Chain B: M.40, G.41, R.74 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.41, B:G.41 Salt bridges: B:R.74 SO4.6: 4 residues within 4Å: Chain A: Q.37 Chain B: F.167, P.168, G.169 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.169, A:Q.37 SO4.7: 3 residues within 4Å: Chain A: R.116 Chain B: R.116 Chain D: T.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.116, A:R.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newman, M. et al., Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition. EMBO J. (2005)

Release Date

2005-02-23

Peptides

XPF ENDONUCLEASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

XPF ENDONUCLEASE