SMTL ID : 5zai.1

Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 17 residues within 4Å: Chain A: D.23, K.24, L.25, A.27, A.63, A.65, D.66, I.67, F.70, Y.106, L.108, P.132, E.133, L.136, R.166 Chain C: F.248, K.251 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.25, A:L.108 Hydrogen bonds: A:A.63, A:A.65, A:I.67, C:K.251 Water bridges: A:Y.106, C:K.251 Salt bridges: A:K.24, C:K.251 pi-Stacking: C:F.248, C:F.248 COA.8: 17 residues within 4Å: Chain A: F.248, K.251 Chain B: D.23, K.24, L.25, K.59, A.63, G.64, A.65, D.66, I.67, F.70, Y.106, L.108, P.132, E.133, R.166 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.63, B:Y.106, B:L.108 Hydrogen bonds: B:K.24, B:A.63, B:A.63, B:I.67 Salt bridges: B:K.24, B:K.59, A:K.251 COA.11: 17 residues within 4Å: Chain B: F.248, K.251 Chain C: D.23, K.24, L.25, A.27, A.63, G.64, A.65, D.66, I.67, L.108, G.109, G.110, P.132, E.133, R.166 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.25, C:A.63, C:I.67, C:L.108 Hydrogen bonds: C:A.63, C:A.63, C:I.67 Salt bridges: C:K.24, B:K.251 COA.21: 15 residues within 4Å: Chain D: F.248 Chain E: D.23, K.24, L.25, A.27, A.63, G.64, A.65, D.66, I.67, Y.106, L.108, P.132, E.133, R.166 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:L.25, E:L.108, D:F.248 Hydrogen bonds: E:A.63, E:I.67 Water bridges: E:P.132 Salt bridges: E:K.24, E:K.59

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

EDO.2: 5 residues within 4Å: Chain A: E.93, R.147, N.214 Chain B: K.154 Chain C: L.221 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.147, A:N.214, B:K.154 EDO.3: 3 residues within 4Å: Chain A: R.21, D.23, K.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.21 EDO.4: 6 residues within 4Å: Chain A: K.59, G.105, Y.106, E.126, A.127, Q.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.128 EDO.5: 6 residues within 4Å: Chain A: T.74, A.76 Chain D: I.204, S.237, T.238, E.239 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.239, A:T.74 Water bridges: D:D.240, A:A.76 EDO.9: 6 residues within 4Å: Chain B: K.59, G.105, Y.106, E.126, A.127, Q.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.128 EDO.12: 5 residues within 4Å: Chain B: N.179, R.180 Chain C: R.156, E.159, M.160 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:Y.175 Hydrogen bonds: B:N.179, B:R.180 EDO.15: 7 residues within 4Å: Chain D: E.113, E.133, I.138, P.140, G.141, Y.142 Chain F: W.232 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:W.232, D:E.113, D:G.141, D:Y.142 EDO.16: 5 residues within 4Å: Chain D: N.13, L.14, E.196, A.199, K.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.13 Water bridges: D:N.13 EDO.17: 5 residues within 4Å: Chain D: R.156, E.159, M.160, Y.175 Chain F: N.179 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.156, F:N.179 EDO.23: 6 residues within 4Å: Chain E: N.179 Chain F: R.156, E.159, M.160, I.167, Y.175 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.179 EDO.24: 5 residues within 4Å: Chain F: K.9, W.16, T.18, T.55, E.188 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.9, F:T.18, F:T.18, F:E.188, F:R.192

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.9, E.11, W.16, T.18, T.55, E.188, R.192 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.9, A:K.9, A:E.11, A:T.18, A:R.192 GOL.7: 6 residues within 4Å: Chain A: R.156, E.159, M.160, I.167, D.171, Y.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.171, A:Y.175 GOL.10: 7 residues within 4Å: Chain A: N.179, R.180 Chain B: R.156, E.159, M.160, I.167, Y.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.179, A:R.180 GOL.13: 6 residues within 4Å: Chain A: K.154 Chain C: E.93, R.147, R.150, N.214, L.217 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.214 Water bridges: C:E.93, C:R.150 GOL.14: 6 residues within 4Å: Chain C: F.236, S.237, T.238, E.239, K.241, K.242 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.241, C:K.241 GOL.18: 6 residues within 4Å: Chain D: E.11, W.16, T.18, T.55, E.188, R.192 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.11, D:T.18, D:R.192 GOL.19: 6 residues within 4Å: Chain D: E.93, R.147, R.150, L.217 Chain E: K.154 Chain F: L.221 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:K.154, D:E.93, D:R.147 Water bridges: D:R.150 GOL.20: 1 residues within 4Å: Chain D: K.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.9 GOL.22: 8 residues within 4Å: Chain D: N.179, R.180 Chain E: R.156, E.159, M.160, D.165, I.167, Y.175 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:N.179, D:R.180, E:D.165, E:D.165, E:Y.175, E:Y.175 GOL.25: 6 residues within 4Å: Chain D: L.221 Chain E: E.93, R.147, R.150, N.214 Chain F: K.154 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.154 Water bridges: F:K.154, E:E.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, D. et al., Structural Insight into Substrate Specificity of 3-Hydroxypropionyl-Coenzyme A Dehydratase from Metallosphaera sedula. Sci Rep (2018)

Release Date

2018-08-01

Peptides

3-hydroxypropionyl-coenzyme A dehydratase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

3-hydroxypropionyl-coenzyme A dehydratase