SMTL ID : 5lbx.1

Structure of the T175V Etr1p mutant in the trigonal form P312 in complex with NADP and crotonyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 21 residues within 4Å: Chain A: P.68, V.170, N.171, V.174, G.196, T.198, S.199, A.200, V.201, R.221, R.223, C.273, V.274, Y.295, G.296, M.298, F.320, W.321, V.322, K.380 Ligands: COO.10 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.170, A:V.174 Hydrogen bonds: A:N.171, A:G.196, A:T.198, A:T.198, A:A.200, A:V.201, A:C.273, A:Y.295, A:G.297, A:M.298, A:V.322 Water bridges: A:T.198, A:T.198, A:K.380, A:K.380, A:K.380, A:K.380 Salt bridges: A:R.221, A:R.223, A:K.380, A:K.380 pi-Cation interactions: A:R.221, A:R.221 NAP.12: 22 residues within 4Å: Chain B: P.68, V.170, N.171, V.174, T.198, S.199, A.200, V.201, R.221, R.223, C.273, V.274, Y.295, G.296, M.298, S.299, F.320, W.321, V.322, K.380 Ligands: SO4.16, COO.18 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.170, B:V.174 Hydrogen bonds: B:N.171, B:T.198, B:T.198, B:T.198, B:A.200, B:V.201, B:C.273, B:Y.295, B:G.297, B:V.322 Water bridges: B:R.221, B:R.223, B:R.223 Salt bridges: B:R.221, B:R.223, B:K.380, B:K.380 pi-Cation interactions: B:R.221, B:R.221

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: S.124, H.125, V.126, T.323, K.327, K.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.126 Salt bridges: A:H.125, A:K.330, A:K.333 SO4.3: 3 residues within 4Å: Chain A: S.249, R.250, E.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.250, A:E.251 SO4.4: 3 residues within 4Å: Chain A: V.230, V.241, Q.246 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.246, A:Q.246 Water bridges: A:V.241, A:V.241 SO4.5: 3 residues within 4Å: Chain A: K.144, Q.150, N.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.154, A:N.154 Salt bridges: A:K.144 SO4.6: 3 residues within 4Å: Chain A: Q.32, H.33, K.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.33 Water bridges: A:K.84 Salt bridges: A:H.33, A:K.84 SO4.7: 3 residues within 4Å: Chain A: R.223, N.225, V.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.225 Salt bridges: A:R.223 SO4.8: 1 residues within 4Å: Chain A: Q.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.262 SO4.9: 2 residues within 4Å: Chain A: N.287, N.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.287, A:N.288 Water bridges: A:L.286 SO4.13: 3 residues within 4Å: Chain B: Q.32, H.33, K.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.33 Salt bridges: B:H.33, B:K.84 SO4.14: 4 residues within 4Å: Chain B: L.226, V.241, I.242, Q.246 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.241, B:Q.246 Water bridges: B:D.227, B:V.241 SO4.15: 3 residues within 4Å: Chain B: R.223, N.225, V.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.225, B:N.225 Salt bridges: B:R.223 SO4.16: 3 residues within 4Å: Chain B: R.221, K.377 Ligands: NAP.12 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.221, B:K.377 SO4.17: 2 residues within 4Å: Chain B: N.287, N.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.287, B:N.288

2 x COO: CROTONYL COENZYME A(Non-covalent)

COO.10: 14 residues within 4Å: Chain A: S.69, N.72, Y.78, G.296, G.297, F.300, W.321, V.322, T.323 Chain B: R.284, P.306, T.307, S.308 Ligands: NAP.1 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.284, B:T.307, B:T.307, B:T.307, B:S.308, B:S.308, B:S.308, A:N.72, A:N.72, A:G.297, A:G.297 Hydrophobic interactions: A:V.322 Water bridges: A:S.69 COO.18: 15 residues within 4Å: Chain A: P.306, T.307, S.308, I.311 Chain B: S.69, N.72, Y.78, Y.295, G.296, G.297, M.298, F.300, W.321, T.323 Ligands: NAP.12 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.78, A:T.307 Hydrogen bonds: B:N.72, B:G.297, A:R.284, A:T.307, A:S.308, A:S.308, A:S.308 Water bridges: B:S.69

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 1 residues within 4Å: Chain A: K.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosenthal, R.G. et al., A conserved threonine prevents self-intoxication of enoyl-thioester reductases. Nat. Chem. Biol. (2017)

Release Date

2017-05-10

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial

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