SMTL ID : 4ws6.1

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-aminouracil, Form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x WBU: 5-AMINO-1H-PYRIMIDINE-2,4-DIONE(Non-covalent)

WBU.1: 11 residues within 4Å: Chain A: G.77, Q.78, D.79, P.80, Y.81, S.91, F.92, N.138, H.202 Ligands: CIT.2, EDO.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.78, A:D.79, A:F.92, A:N.138, A:N.138, A:H.202 Water bridges: A:Y.81, A:Y.81 pi-Stacking: A:Y.81, A:F.92

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 7 residues within 4Å: Chain A: Y.81, P.82, T.83, P.102, R.103, S.104 Ligands: WBU.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.82 Hydrogen bonds: A:R.103, A:R.103, A:S.104 Water bridges: A:T.83, A:T.83 Salt bridges: A:R.103 CIT.3: 6 residues within 4Å: Chain A: Q.78, G.180, R.181, L.206, R.210 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.181 Water bridges: A:Q.78, A:D.182, A:H.202, A:S.204, A:R.210 Salt bridges: A:R.210

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

EDO.4: 5 residues within 4Å: Chain A: Q.78, H.202, S.204 Ligands: WBU.1, CIT.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.202 Water bridges: A:Q.78, A:Q.78, A:Q.78, A:Q.78, A:S.204

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

DMS.5: 2 residues within 4Å: Chain A: G.50, R.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.52 DMS.6: 3 residues within 4Å: Chain A: I.47, R.52, Y.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.53 pi-Cation interactions: A:Y.53 DMS.7: 3 residues within 4Å: Chain A: P.100, W.101, A.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.101 DMS.8: 2 residues within 4Å: Chain A: T.65, F.66 No protein-ligand interaction detected (PLIP)

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.9: 2 residues within 4Å: Chain A: Q.131, R.132 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.132 Water bridges: A:N.70

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

CL.10: 1 residues within 4Å: Chain A: R.51 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.51, R.52, R.144 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arif, S.M. et al., Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-07-15

Peptides

Uracil-DNA glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uracil-DNA glycosylase

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