SMTL ID : 4a15.1

Crystal structure of an XPD DNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DT- DA- DC- DG: 5'-D(*DTP*AP*CP*GP)-3'(Non-covalent)

DT-DA-DC-DG.1: 10 residues within 4Å: Chain A: P.456, F.527, P.528, R.529, P.530, N.534, R.535, F.538, W.549, R.584 Protein-ligand interaction information (PLIP) not available

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 9 residues within 4Å: Chain A: R.88, C.92, I.93, L.94, C.113, C.128, F.131, C.164, E.167 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.167 Metal complexes: A:C.92, A:C.113, A:C.128, A:C.164

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

SO4.3: 7 residues within 4Å: Chain A: P.30, T.31, G.32, S.33, G.34, K.35, Q.66 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.32, A:G.32, A:S.33, A:G.34, A:K.35 Water bridges: A:T.36, A:R.567 Salt bridges: A:K.35 SO4.4: 6 residues within 4Å: Chain A: R.88, A.110, Y.166, K.170, K.194, H.198 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.166, A:Y.166 Water bridges: A:R.88, A:R.88 Salt bridges: A:R.88, A:K.170, A:H.198 SO4.5: 3 residues within 4Å: Chain A: S.255, E.259, R.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.259, A:R.262 Salt bridges: A:D.237, A:E.259

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.107, K.111, E.312, E.315 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.312, A:E.315, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuper, J. et al., Functional and Structural Studies of the Nucleotide Excision Repair Helicase Xpd Suggest a Polarity for DNA Translocation. Embo J. (2011)

Release Date

2012-02-01

Peptides

ATP-DEPENDENT DNA HELICASE TA0057: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-DEPENDENT DNA HELICASE TA0057