SMTL ID : 8am8.1

Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate - W113A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 40 residues within 4Å: Chain A: V.74, G.75, S.76, G.77, C.78, A.79, L.97, E.98, K.99, G.104, G.105, T.106, T.107, K.109, S.110, A.111, F.112, A.113, H.245, R.246, V.247, G.282, S.283, G.284, C.305, T.309, N.310, D.313, S.349, F.352, L.530, G.559, N.560, Y.570, G.574, A.575, T.576, L.577, M.580 Ligands: A2Q.8 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.352, A:L.530 Hydrogen bonds: A:G.77, A:A.79, A:K.99, A:K.99, A:G.104, A:T.106, A:T.107, A:T.107, A:A.111, A:A.113, A:A.113, A:V.247, A:V.247, A:T.309, A:N.310, A:D.313, A:N.560, A:N.560, A:Y.570, A:G.574, A:T.576, A:T.576, A:L.577 Water bridges: A:G.80, A:G.105, A:G.284, A:G.284, A:G.285, A:E.311, A:D.531 pi-Stacking: A:F.352 FAD.10: 40 residues within 4Å: Chain B: V.74, G.75, S.76, G.77, C.78, A.79, L.97, E.98, K.99, G.104, G.105, T.106, T.107, K.109, S.110, A.111, F.112, A.113, H.245, R.246, V.247, G.282, S.283, G.284, C.305, T.309, N.310, D.313, S.349, F.352, L.530, G.559, N.560, Y.570, G.574, A.575, T.576, L.577, M.580 Ligands: A2Q.15 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:F.352, B:L.530 Hydrogen bonds: B:G.77, B:C.78, B:A.79, B:K.99, B:K.99, B:G.104, B:T.106, B:T.106, B:T.107, B:T.107, B:A.111, B:A.113, B:A.113, B:V.247, B:V.247, B:T.309, B:T.309, B:N.310, B:N.560, B:N.560, B:Y.570, B:G.574, B:T.576, B:L.577 Water bridges: B:G.80, B:G.105, B:G.285, B:G.285, B:E.311, B:C.561 pi-Stacking: B:F.352

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: M.163, V.558, G.559, V.562, A.563, S.564, M.580, F.583 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.559, A:A.565 Water bridges: A:T.576 GOL.3: 9 residues within 4Å: Chain A: T.142, R.143, P.144, Q.145, H.330, S.567, G.568 Chain B: P.300, Y.393 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.143, A:R.143, A:Q.145, A:H.330, A:G.568, B:Y.393 GOL.4: 6 residues within 4Å: Chain A: Q.407, V.420, D.426, V.429, K.431, Y.521 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.407, A:Q.407, A:D.426 GOL.5: 5 residues within 4Å: Chain A: E.385, W.386 Chain B: Q.381, K.382, E.385 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.385, A:W.386 Water bridges: A:W.386, A:G.388, B:K.382 GOL.6: 4 residues within 4Å: Chain A: A.67, E.68, Y.69 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68, A:E.68 GOL.11: 9 residues within 4Å: Chain B: M.163, V.558, G.559, V.562, A.563, S.564, A.565, M.580, F.583 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.559, B:A.563, B:A.565 Water bridges: B:G.557, B:G.559, B:T.576 GOL.12: 9 residues within 4Å: Chain A: P.300, Y.393 Chain B: T.142, R.143, P.144, Q.145, H.330, S.567, G.568 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.142, B:R.143, B:Q.145, B:H.330, B:G.568, A:Y.393, A:Y.393 GOL.13: 5 residues within 4Å: Chain B: P.149, E.150, H.151, P.152, L.154 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: T.157, W.159, E.160 Chain B: E.291, N.295 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.295, A:T.157 Water bridges: A:T.157, A:N.327, A:S.567 PEG.14: 7 residues within 4Å: Chain A: L.292, V.315, R.316 Chain B: V.323, Q.324, L.325, R.326 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.316, B:L.325, B:R.326, B:R.326 Water bridges: A:D.289

2 x A2Q: cyclohex-2-en-1-one(Non-covalent)

A2Q.8: 8 residues within 4Å: Chain A: Y.195, F.352, Y.376, F.496, Y.570, G.573, G.574 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.496 Hydrogen bonds: A:Y.195, A:Y.376, A:G.574 pi-Stacking: A:F.352 A2Q.15: 8 residues within 4Å: Chain B: Y.195, F.352, Y.376, L.530, Y.570, G.573, G.574 Ligands: FAD.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.530 Hydrogen bonds: B:Y.570, B:G.574 pi-Stacking: B:F.352

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

SO4.9: 5 residues within 4Å: Chain A: E.68, Y.69, S.93, R.276 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.68, A:S.93 Salt bridges: A:R.276 SO4.16: 2 residues within 4Å: Chain B: H.409, K.501 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.409, B:K.501 SO4.17: 3 residues within 4Å: Chain B: D.436, N.463, R.467 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.463, B:A.464 Water bridges: B:N.463, B:N.463 Salt bridges: B:R.467

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, W. et al., Rational design of a cyclohexanone dehydrogenase for enhanced alpha , beta-desaturation and substrate specificity. Chem Sci (2024)

Release Date

2024-02-14

Peptides

Fumarate reductase/succinate dehydrogenase flavoprotein domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

B
AAA

Fumarate reductase/succinate dehydrogenase flavoprotein domain protein