SMTL ID : 4iv6.1

X-ray crystal structure of an isovaleryl-CoA dehydrogenase from Mycobacterium smegmatis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.1: 34 residues within 4Å: Chain A: M.124, A.125, L.126, T.127, G.131, G.132, S.133, W.157, I.158, S.159, K.203, Y.206, S.211, L.361, V.364, G.365, G.367, T.368, E.370, I.371, N.374 Chain B: R.271, S.273, F.274, I.278, H.281, S.283, V.284, R.339, V.340, G.342, G.343, Y.344 Chain D: Q.282 36 PLIP interactions: 27 interactions with chain A, 8 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:W.157, A:W.157, A:W.157, A:K.203, A:Y.206, A:L.361 Hydrogen bonds: A:M.124, A:L.126, A:T.127, A:T.127, A:T.127, A:G.132, A:S.133, A:S.159, A:S.159, A:G.365, A:G.367, A:T.368, A:T.368, A:N.374, B:S.273, B:R.339, B:G.343, D:Q.282 Water bridges: A:M.124, A:T.127, A:G.131, A:G.132, A:G.132, A:S.159, A:T.368, B:R.271, B:R.271, B:R.271 Salt bridges: B:R.271, B:R.271 FDA.2: 32 residues within 4Å: Chain A: R.271, S.273, F.274, I.278, H.281, S.283, V.284, R.339, V.340, G.342, G.343 Chain B: M.124, L.126, T.127, G.131, G.132, S.133, W.157, I.158, S.159, K.203, Y.206, S.211, L.361, V.364, G.365, G.367, T.368, E.370, I.371, N.374 Chain C: Q.282 34 PLIP interactions: 25 interactions with chain B, 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:W.157, B:W.157, B:K.203, B:Y.206, B:L.361 Hydrogen bonds: B:M.124, B:L.126, B:T.127, B:T.127, B:T.127, B:T.127, B:G.132, B:S.133, B:S.133, B:S.159, B:S.159, B:G.365, B:G.367, B:T.368, B:T.368, B:N.374, A:S.273, A:R.339, A:G.343, C:Q.282 Water bridges: B:M.124, B:S.133, B:S.159, B:T.368, A:R.271, A:R.271, A:R.271 Salt bridges: A:R.271, A:R.271 FDA.3: 34 residues within 4Å: Chain B: Q.282 Chain C: M.124, A.125, L.126, T.127, G.131, G.132, S.133, W.157, I.158, S.159, K.203, Y.206, S.211, L.361, V.364, G.365, G.367, T.368, E.370, I.371, N.374 Chain D: R.271, S.273, F.274, I.278, H.281, S.283, V.284, R.339, V.340, G.342, G.343, Y.344 37 PLIP interactions: 28 interactions with chain C, 1 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: C:W.157, C:W.157, C:W.157, C:K.203, C:Y.206, C:L.361 Hydrogen bonds: C:M.124, C:L.126, C:T.127, C:T.127, C:T.127, C:G.132, C:S.133, C:S.159, C:S.159, C:G.365, C:G.367, C:T.368, C:E.370, C:N.374, B:Q.282, D:S.273, D:R.339, D:G.343 Water bridges: C:T.123, C:M.124, C:T.127, C:G.131, C:G.132, C:G.132, C:S.159, C:T.368, D:R.271, D:R.271, D:R.271 Salt bridges: D:R.271, D:R.271 FDA.4: 32 residues within 4Å: Chain A: Q.282 Chain C: R.271, S.273, F.274, I.278, H.281, S.283, V.284, R.339, V.340, G.342, G.343 Chain D: M.124, L.126, T.127, G.131, G.132, S.133, W.157, I.158, S.159, K.203, Y.206, S.211, L.361, V.364, G.365, G.367, T.368, E.370, I.371, N.374 35 PLIP interactions: 26 interactions with chain D, 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:W.157, D:W.157, D:K.203, D:Y.206, D:L.361 Hydrogen bonds: D:M.124, D:L.126, D:T.127, D:T.127, D:T.127, D:T.127, D:G.132, D:S.133, D:S.133, D:S.159, D:S.159, D:G.365, D:G.367, D:T.368, D:E.370, D:N.374, C:S.273, C:R.339, C:G.343, A:Q.282 Water bridges: D:T.123, D:M.124, D:S.133, D:S.159, D:T.368, C:R.271, C:R.271, C:R.271 Salt bridges: C:R.271, C:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2013-03-20

Peptides

Acyl-CoA dehydrogenase FadE3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acyl-CoA dehydrogenase FadE3