SMTL ID : 3p4t.1

Crystal structure of a putative acyl-CoA dehydrogenase from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: Q.276, A.310, D.314, R.317 Chain D: F.340, L.399 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.276, A:Q.276, A:R.317, A:R.317 EDO.4: 5 residues within 4Å: Chain B: Q.276, A.310, D.314, R.317 Chain C: L.399 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.276, B:Q.276, B:R.317, B:R.317 EDO.5: 6 residues within 4Å: Chain B: F.340, L.399 Chain C: Q.276, A.310, D.314, R.317 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.276, C:Q.276, C:R.317, C:R.317 EDO.8: 5 residues within 4Å: Chain A: L.399 Chain D: Q.276, A.310, D.314, R.317 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.276, D:Q.276, D:R.317, D:R.317

4 x FAO: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate

FAO.2: 28 residues within 4Å: Chain A: I.115, L.145, A.146, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, I.380, I.383, G.385, T.387, E.389 Chain B: R.289, T.291, F.292, L.296, R.299, Q.358, L.359, G.361, G.362, M.366 Chain D: Q.300 32 PLIP interactions: 22 interactions with chain A, 9 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:Y.178, A:K.222, A:I.380 Hydrogen bonds: A:L.145, A:I.147, A:T.148, A:T.148, A:G.153, A:S.154, A:S.154, A:T.180, A:T.180, A:T.180, A:G.385, A:T.387, A:T.387, A:E.389, B:T.291, B:T.291, B:Q.358, B:G.362, D:Q.300 Water bridges: A:T.148, A:E.149, A:G.153, A:G.386, A:G.386, B:R.289, B:R.299, B:M.363 Salt bridges: B:R.289, B:R.289 FAO.3: 26 residues within 4Å: Chain A: R.289, T.291, F.292, L.296, R.299, V.302, Q.358, L.359, G.361, G.362, M.366 Chain B: L.145, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, I.380, I.383, T.387, E.389 Chain C: Q.300 29 PLIP interactions: 19 interactions with chain B, 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:Y.178, B:K.222, B:I.380 Hydrogen bonds: B:L.145, B:I.147, B:T.148, B:T.148, B:T.148, B:G.153, B:S.154, B:S.154, B:T.180, B:T.180, B:G.385, B:T.387, A:T.291, A:T.291, A:Q.358, A:G.362, C:Q.300 Water bridges: B:T.180, B:T.180, B:G.386, B:G.386, A:R.289, A:R.289, A:M.363 Salt bridges: A:R.289, A:R.289 FAO.6: 28 residues within 4Å: Chain B: Q.300 Chain C: I.115, L.145, A.146, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, I.380, I.383, G.385, T.387, E.389 Chain D: R.289, T.291, F.292, L.296, R.299, Q.358, L.359, G.361, G.362, M.366 31 PLIP interactions: 22 interactions with chain C, 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:Y.178, C:K.222, C:I.380 Hydrogen bonds: C:L.145, C:I.147, C:T.148, C:T.148, C:T.148, C:G.153, C:S.154, C:S.154, C:T.180, C:T.180, C:G.385, C:T.387, D:T.291, D:T.291, D:Q.358, D:G.362, B:Q.300 Water bridges: C:T.148, C:E.149, C:G.153, C:Y.178, C:Y.178, C:G.386, C:G.386, D:R.289, D:R.299 Salt bridges: D:R.289, D:R.289 FAO.7: 26 residues within 4Å: Chain A: Q.300 Chain C: R.289, T.291, F.292, L.296, R.299, V.302, Q.358, L.359, G.361, G.362, M.366 Chain D: L.145, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, I.380, I.383, T.387, E.389 29 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A, 19 interactions with chain D Hydrogen bonds: C:T.291, C:T.291, C:Q.358, C:G.362, A:Q.300, D:L.145, D:I.147, D:T.148, D:T.148, D:G.153, D:S.154, D:S.154, D:T.180, D:T.180, D:T.180, D:G.385, D:T.387, D:T.387, D:E.389 Water bridges: C:R.289, C:R.289, C:M.363, D:G.386, D:G.386 Salt bridges: C:R.289, C:R.289 Hydrophobic interactions: D:Y.178, D:K.222, D:I.380

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

2010-10-20

Peptides

Putative acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Putative acyl-CoA dehydrogenase

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