SMTL ID : 5jx8.1

New improved structure of D4 in trigonal space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.179, K.180, T.181, G.199, Y.200, H.201, A.204 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.180, A:T.181, A:T.181, A:H.201 Water bridges: A:G.179, A:D.182 SO4.2: 4 residues within 4Å: Chain A: S.23, V.24, T.25 Chain B: I.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.25 Water bridges: A:S.23, A:S.23 SO4.5: 5 residues within 4Å: Chain B: G.179, K.180, T.181, Y.200, H.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.180, B:T.181, B:H.201 Water bridges: B:D.182

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: P.16, R.17, G.18, S.19, H.20 Chain B: P.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17, A:G.18, A:S.19, A:H.20 Water bridges: A:G.18 GOL.4: 6 residues within 4Å: Chain A: D.88, P.89, Y.90, P.98, F.99, N.140 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.88, A:Y.90, A:V.97, A:F.99, A:N.140 Water bridges: A:T.95, A:T.95 GOL.6: 6 residues within 4Å: Chain B: D.88, P.89, Y.90, P.98, F.99, N.140 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.90, B:F.99, B:N.140 Water bridges: B:V.97, B:E.100 GOL.7: 1 residues within 4Å: Chain B: K.107 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.106, B:K.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases. Protein Sci. (2016)

Release Date

2017-02-08

Peptides

Uracil-DNA glycosylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uracil-DNA glycosylase

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