SMTL ID : 4xvx.1 (2 other biounits)

Crystal structure of an acyl-ACP dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.1: 18 residues within 4Å: Chain A: A.78, A.80, V.84, L.88, S.156, I.244, I.248, S.251, A.255, I.326, W.348, D.351, M.352, L.354, A.355, G.358, G.359 Ligands: FDA.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.88 Hydrogen bonds: A:S.251, A:S.251 P33.5: 18 residues within 4Å: Chain C: A.78, A.80, V.84, L.88, S.156, I.244, I.248, S.251, A.255, I.326, W.348, D.351, M.352, L.354, A.355, G.358, G.359 Ligands: FDA.6 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.88 Hydrogen bonds: C:S.251, C:S.251

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

FDA.2: 27 residues within 4Å: Chain A: I.121, G.122, A.123, S.124, G.129, S.130, F.154, S.156, K.200, T.208, L.354, V.357, G.359, T.361, E.363 Chain B: R.266, Q.268, F.269, L.273, H.276, L.279, H.331, I.332, G.334, G.335 Chain D: Q.277 Ligands: P33.1 28 PLIP interactions: 16 interactions with chain A, 10 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:F.154, A:F.154, A:K.200, A:T.208 Hydrogen bonds: A:I.121, A:A.123, A:S.124, A:S.124, A:S.124, A:S.130, A:S.130, A:S.156, A:G.359, A:G.360, A:T.361, A:T.361, B:Q.268, B:H.331, B:G.335, D:Q.277 Water bridges: B:R.262, B:R.266, B:R.266, B:A.336, D:Q.277 Salt bridges: B:R.266, B:R.266 pi-Stacking: B:H.276 FDA.4: 27 residues within 4Å: Chain A: R.266, Q.268, F.269, L.273, H.276, L.279, H.331, I.332, G.334, G.335 Chain B: I.121, A.123, S.124, G.129, S.130, F.154, S.156, K.200, L.354, V.357, G.358, G.359, G.360, T.361, E.363 Chain C: Q.277 Ligands: P6G.3 28 PLIP interactions: 15 interactions with chain B, 12 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:F.154, B:F.154, B:K.200, B:L.354 Hydrogen bonds: B:I.121, B:A.123, B:S.124, B:S.124, B:S.124, B:S.130, B:S.156, B:G.359, B:G.360, B:T.361, B:T.361, A:Q.268, A:H.331, A:G.335, C:Q.277 Water bridges: A:R.262, A:R.266, A:R.266, A:R.266, A:R.266, A:A.336 Salt bridges: A:R.266, A:R.266 pi-Stacking: A:H.276 FDA.6: 27 residues within 4Å: Chain B: Q.277 Chain C: I.121, G.122, A.123, S.124, G.129, S.130, F.154, S.156, K.200, T.208, L.354, V.357, G.359, T.361, E.363 Chain D: R.266, Q.268, F.269, L.273, H.276, L.279, H.331, I.332, G.334, G.335 Ligands: P33.5 27 PLIP interactions: 18 interactions with chain C, 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:F.154, C:F.154, C:K.200, C:T.208 Hydrogen bonds: C:I.121, C:A.123, C:S.124, C:S.124, C:S.124, C:S.130, C:S.130, C:S.156, C:G.359, C:G.360, C:T.361, C:E.363, D:Q.268, D:H.331, D:G.335, B:Q.277 Water bridges: C:E.367, C:E.367, D:R.262, D:A.336 Salt bridges: D:R.266, D:R.266 pi-Stacking: D:H.276 FDA.8: 27 residues within 4Å: Chain A: Q.277 Chain C: R.266, Q.268, F.269, L.273, H.276, L.279, H.331, I.332, G.334, G.335 Chain D: I.121, A.123, S.124, G.129, S.130, F.154, S.156, K.200, L.354, V.357, G.358, G.359, G.360, T.361, E.363 Ligands: P6G.7 28 PLIP interactions: 15 interactions with chain D, 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:F.154, D:F.154, D:K.200, D:L.354 Hydrogen bonds: D:I.121, D:A.123, D:S.124, D:S.124, D:S.124, D:S.130, D:S.156, D:G.359, D:G.360, D:T.361, D:E.363, C:Q.268, C:H.331, C:G.335, A:Q.277 Water bridges: C:R.262, C:R.266, C:R.266, C:R.266, C:R.266, C:A.336 Salt bridges: C:R.266, C:R.266 pi-Stacking: C:H.276

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 15 residues within 4Å: Chain B: A.78, A.80, V.84, L.88, S.156, I.244, I.248, S.251, W.348, D.351, L.354, A.355, G.358, G.359 Ligands: FDA.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.88 Hydrogen bonds: B:S.251, B:S.251 P6G.7: 15 residues within 4Å: Chain D: A.78, A.80, V.84, L.88, S.156, I.244, I.248, S.251, W.348, D.351, L.354, A.355, G.358, G.359 Ligands: FDA.8 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.88 Hydrogen bonds: D:S.251, D:S.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chai, A.F. et al., A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-02-11

Peptides

Acyl-[acyl-carrier-protein] dehydrogenase MbtN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acyl-[acyl-carrier-protein] dehydrogenase MbtN

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