SMTL ID : 4cmv.1

Crystal structure of Rv3378c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

12 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 3 residues within 4Å: Chain A: R.155, C.157, Y.194 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.157, H2O.4 HG.2: 2 residues within 4Å: Chain A: H.41, P.46 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.41 HG.3: 3 residues within 4Å: Chain A: F.67, E.153, H.154 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.67, A:H.154, H2O.1, H2O.3, H2O.6 HG.4: 2 residues within 4Å: Chain A: W.176, H.180 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.180 HG.5: 3 residues within 4Å: Chain A: H.117, N.151, E.196 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.117, A:E.196, A:E.196, H2O.3 HG.6: 3 residues within 4Å: Chain A: H.117, T.145, S.149 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.117 HG.7: 1 residues within 4Å: Chain A: F.293 No protein-ligand interaction detected (PLIP) HG.10: 4 residues within 4Å: Chain B: I.75, R.155, C.157, Y.194 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.157 HG.11: 3 residues within 4Å: Chain B: H.117, N.151, E.196 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.117, B:E.196 HG.12: 2 residues within 4Å: Chain B: F.67, H.154 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.154 HG.13: 1 residues within 4Å: Chain B: H.41 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.41 HG.14: 2 residues within 4Å: Chain B: H.288, F.293 No protein-ligand interaction detected (PLIP)

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

CIT.8: 8 residues within 4Å: Chain A: G.35, T.36, R.37, R.38, F.207, R.209 Chain B: P.257, Y.259 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.35, A:R.37, A:R.37, A:R.38, A:R.38 Water bridges: A:R.38, A:R.209, A:R.209 Salt bridges: A:R.37, A:R.38, A:R.209 CIT.9: 10 residues within 4Å: Chain A: A.165, A.166, V.169, P.216, L.217 Chain B: D.164, A.165, A.166, P.216, L.217 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.216, B:L.217 Hydrogen bonds: B:D.164, B:A.165, B:A.166, B:L.217, A:A.165, A:L.217 Water bridges: B:F.215, B:F.215, B:S.219, B:S.219, A:D.164, A:L.217, A:S.219 CIT.15: 8 residues within 4Å: Chain A: P.257, Y.259 Chain B: G.35, T.36, R.37, R.38, F.207, R.209 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:Y.259, B:G.35, B:R.37, B:R.38, B:R.209 Water bridges: B:D.34, B:D.34, B:R.38 Salt bridges: B:R.37, B:R.37, B:R.38, B:R.209

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

DITERPENE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DITERPENE SYNTHASE

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