SMTL ID : 5yhv.1

Crystal structure of an aminotransferase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 8 residues within 4Å: Chain A: D.86, Y.87, H.91, H.212, G.213, N.236, Y.242, W.251 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:H.212 Hydrogen bonds: A:H.212, A:N.236, A:N.236 Water bridges: A:Y.87, A:E.209 Salt bridges: A:H.91, A:H.212

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: V.215, Y.216, Q.217, L.297, A.298, A.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.215, A:Q.217 Water bridges: A:A.298 GOL.5: 5 residues within 4Å: Chain B: R.313, I.314, E.381, L.384, R.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.313 Water bridges: B:R.385 GOL.7: 5 residues within 4Å: Chain A: A.61, L.65 Chain C: A.57, A.58, A.61 3 PLIP interactions: 3 interactions with chain C Water bridges: C:P.54, C:A.58, C:S.283

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.3: 15 residues within 4Å: Chain A: G.105, S.106, S.107, Y.131, Y.134, N.180, D.208, Y.211, S.237, S.239, K.240, R.248, Y.327 Chain B: Y.70, I.271 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.131, A:N.180, A:Y.211, A:K.240 Hydrogen bonds: A:S.106, A:S.107, A:N.180, A:Y.211, A:S.237, A:S.237, A:S.239, A:Y.327 Salt bridges: A:K.240, A:R.248 pi-Stacking: A:Y.131 PLP.4: 15 residues within 4Å: Chain A: Y.70, I.271 Chain B: G.105, S.106, S.107, Y.131, Y.134, N.180, D.208, V.210, Y.211, S.237, S.239, K.240, R.248 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.131, B:V.210, B:K.240 Hydrogen bonds: B:S.106, B:S.106, B:S.106, B:S.107, B:N.180, B:Y.211, B:S.237, B:S.239 Salt bridges: B:K.240, B:R.248 pi-Stacking: B:Y.131 PLP.9: 15 residues within 4Å: Chain C: G.45, G.105, S.106, S.107, Y.131, Y.134, N.180, D.208, Y.211, S.237, S.239, K.240, R.248 Chain D: Y.70, I.271 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.131, C:N.180, C:K.240 Hydrogen bonds: C:S.106, C:S.106, C:S.107, C:N.180, C:S.237, C:S.239, C:K.240, D:Y.70 Salt bridges: C:K.240, C:R.248 pi-Stacking: C:Y.131 PLP.10: 16 residues within 4Å: Chain C: Y.70, I.271 Chain D: G.105, S.106, S.107, Y.131, Y.134, N.180, D.208, V.210, Y.211, S.237, S.239, K.240, R.248, Y.327 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.131, D:N.180, D:V.210, D:Y.211, D:K.240 Hydrogen bonds: D:S.106, D:S.107, D:S.107, D:Y.134, D:N.180, D:S.237, D:S.239, D:S.239, D:K.240, D:Y.327 Salt bridges: D:K.240, D:R.248 pi-Stacking: D:Y.131

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.6: 10 residues within 4Å: Chain B: D.86, Y.87, H.91, E.209, H.212, T.222, S.223, C.224, Q.227, N.236 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.91 Hydrogen bonds: B:Y.87, B:E.209, B:H.212, B:T.222, B:C.224, B:N.236 Salt bridges: B:H.91, B:H.91, B:H.212 AKG.8: 7 residues within 4Å: Chain C: D.86, Y.87, R.90, H.91, H.212, N.236, Y.242 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:H.212 Hydrogen bonds: C:N.236 Water bridges: C:C.224 Salt bridges: C:R.90, C:H.91, C:H.91, C:H.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saroj, D.C. et al., Crystal structure of an aminotransferase from Mycobacterium tuberculosis. To Be Published

Release Date

2018-10-10

Peptides

Aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aminotransferase