SMTL ID : 3h87.1

Rv0301 Rv0300 Toxin Antitoxin Complex from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

hetero-4-4-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: P.88, R.89, D.92 Chain B: Y.85 Chain C: A.37, Q.41 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.41 Water bridges: C:Q.41, C:Q.41 GOL.2: 4 residues within 4Å: Chain A: D.36, W.40, R.43, E.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.43, A:R.43, A:E.147 GOL.4: 6 residues within 4Å: Chain B: R.20, S.124 Chain C: I.20, Y.31 Chain H: A.43 Ligands: GOL.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.20, B:R.20, C:Y.31 Water bridges: B:S.124 GOL.5: 4 residues within 4Å: Chain B: D.36, W.40, R.43, E.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.43, B:R.43, B:E.147 GOL.8: 7 residues within 4Å: Chain B: E.84 Chain C: L.24, Y.31, R.34, R.35, Q.38 Ligands: GOL.4 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:Q.38, B:E.84 Water bridges: C:R.34, B:Y.85, B:Y.85, B:Y.85, B:S.124, B:S.124 GOL.9: 6 residues within 4Å: Chain E: P.88, R.89, D.92 Chain F: Y.85 Chain G: A.37, Q.41 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain G Hydrogen bonds: E:D.92, G:Q.41 Water bridges: G:Q.41, G:Q.41 GOL.10: 4 residues within 4Å: Chain E: D.36, W.40, R.43, E.147 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.43, E:R.43, E:E.147 GOL.12: 6 residues within 4Å: Chain D: A.43 Chain F: R.20, S.124 Chain G: I.20, Y.31 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.20, F:R.20 Water bridges: F:S.124 GOL.13: 4 residues within 4Å: Chain F: D.36, W.40, R.43, E.147 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.43, F:R.43, F:E.147 GOL.16: 7 residues within 4Å: Chain F: E.84 Chain G: L.24, Y.31, R.34, R.35, Q.38 Ligands: GOL.12 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:E.84, G:Q.38 Water bridges: F:Y.85, F:Y.85, F:Y.85, F:S.124, F:S.124, G:R.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.114, D.132, D.134 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.114, A:D.132, A:D.134, H2O.1, H2O.1, H2O.12 MG.11: 3 residues within 4Å: Chain E: D.114, D.132, D.134 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.114, E:D.132, E:D.134, H2O.18, H2O.18, H2O.29

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 3 residues within 4Å: Chain B: D.132, K.133, R.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.148, B:R.148 BME.14: 3 residues within 4Å: Chain F: D.132, K.133, R.148 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.148, F:R.148

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 4 residues within 4Å: Chain B: E.45, R.46, G.47 Chain C: R.44 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:E.45, B:E.45, C:A.43, C:A.43 IMD.15: 4 residues within 4Å: Chain F: E.45, R.46, G.47 Chain G: R.44 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Water bridges: G:A.43, G:A.43, F:E.45, F:E.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, A.B. et al., The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg(2+) ion in the active site and a putative RNA-binding site. Protein Sci. (2012)

Release Date

2009-05-05

Peptides

Putative uncharacterized protein: ABEF
Putative uncharacterized protein: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

Putative uncharacterized protein

Putative uncharacterized protein