SMTL ID : 4lzb.5 (5 other biounits)

Uracil binding pocket in Vaccinia virus uracil DNA glycosylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: Y.90, K.107, S.108 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: G.179, K.180, Y.200, H.201, A.204 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 7 residues within 4Å: Chain A: I.87, Y.141, Y.142, D.182, N.185, I.186, K.189 No protein-ligand interaction detected (PLIP) DMS.9: 7 residues within 4Å: Chain B: I.87, Y.141, Y.142, D.182, N.185, I.186, K.189 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: D.88, P.89, T.150 Ligands: URA.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.88, H2O.6 K.10: 4 residues within 4Å: Chain B: D.88, P.89, T.150 Ligands: URA.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.88, H2O.10, H2O.10, H2O.10

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

EDO.4: 3 residues within 4Å: Chain A: I.123, D.124, Y.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.125, A:Y.125 Water bridges: A:S.117 EDO.7: 3 residues within 4Å: Chain A: E.52, S.55, W.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55, A:W.56 Water bridges: A:S.55

2 x URA: URACIL(Non-covalent)

URA.6: 10 residues within 4Å: Chain A: G.86, I.87, D.88, P.89, Y.90, P.98, F.99, N.140, H.201 Ligands: K.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.87, A:D.88, A:F.99, A:N.140, A:N.140, A:H.201 Water bridges: A:Y.90 pi-Stacking: A:Y.90, A:F.99 URA.8: 11 residues within 4Å: Chain B: G.86, I.87, D.88, P.89, Y.90, P.98, F.99, S.108, N.140, H.201 Ligands: K.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.87, B:D.88, B:F.99, B:N.140, B:N.140, B:H.201 Water bridges: B:Y.90 pi-Stacking: B:Y.90, B:F.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., Structure of the uracil complex of Vaccinia virus uracil DNA glycosylase. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-12-11

Peptides

Uracil-DNA glycosylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
J

Uracil-DNA glycosylase

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