SMTL ID : 4cmx.1

Crystal structure of Rv3378c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

3 x BHC: BENZENE HEXACARBOXYLIC ACID(Non-covalent)

BHC.1: 11 residues within 4Å: Chain A: R.37, R.38, D.85, R.86, R.89, R.209 Chain B: K.256, P.257, Y.259 Ligands: PEG.4, EDO.6 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.85, A:D.85, A:R.86, B:Y.259 Water bridges: A:R.38, A:R.209 Salt bridges: A:R.37, A:R.37, A:R.37, A:R.38, A:R.38, A:R.86, A:R.86, A:R.89, A:R.89, A:R.209, B:K.256, B:K.256, B:K.256 pi-Cation interactions: A:R.37 Hydrophobic interactions: B:K.256 BHC.2: 5 residues within 4Å: Chain A: H.252, R.254, K.256 Chain B: R.89 Ligands: BHC.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.252, A:R.254, A:R.254, A:K.256, A:K.256, B:R.89 pi-Cation interactions: A:R.254 BHC.5: 11 residues within 4Å: Chain A: K.256, P.257, Y.259 Chain B: R.37, R.38, D.85, R.86, R.89, R.209 Ligands: BHC.2, EDO.7 25 PLIP interactions: 17 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.85, B:D.85, B:R.86 Water bridges: B:R.37, B:R.209, B:R.209, A:K.256, A:Y.259, A:Y.259, A:Y.259 Salt bridges: B:R.37, B:R.37, B:R.37, B:R.38, B:R.38, B:R.86, B:R.86, B:R.89, B:R.89, B:R.209, A:K.256, A:K.256, A:K.256 pi-Cation interactions: B:R.37 Hydrophobic interactions: A:K.256

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

EDO.3: 4 residues within 4Å: Chain A: G.221, K.222, S.224, R.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.224, A:R.251 EDO.6: 3 residues within 4Å: Chain B: K.256, P.257 Ligands: BHC.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.257 EDO.7: 4 residues within 4Å: Chain B: R.37, R.89, Q.93 Ligands: BHC.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.37, B:R.89, B:Q.93, B:Q.93 Water bridges: B:D.88

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: R.37, H.41 Chain B: P.257, D.258, Y.259, S.260 Ligands: BHC.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.257, B:D.258, B:Y.259, A:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Layre, E. et al., Molecular Profiling of Mycobacterium Tuberculosis Identifies Tuberculosinyl Nucleoside Products of the Virulence-Associated Enzyme Rv3378C. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-02-19

Peptides

RV3378C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RV3378C

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