SMTL ID : 8agp.1

Halogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

4 x M1U: (1~{S},2~{S},4~{R})-2-chloranyl-1-methyl-4-prop-1-en-2-yl-cyclohexan-1-ol(Non-covalent)

M1U.1: 11 residues within 4Å: Chain A: D.101, W.102, I.105, A.126, P.127, Y.132, Y.148, Y.209, L.213, A.243, H.270 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.102, A:I.105, A:I.105, A:Y.132, A:Y.132, A:L.213, A:L.213, A:A.243 Hydrogen bonds: A:Y.148 M1U.2: 11 residues within 4Å: Chain A: F.34, P.35, D.101, W.147, Y.148, L.170, M.173, S.177, A.243, H.270, W.271 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.34, A:W.147, A:Y.148, A:Y.148, A:L.170, A:M.173 M1U.13: 9 residues within 4Å: Chain B: D.101, W.102, I.105, P.127, Y.132, Y.148, L.213, A.243, I.244 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.102, B:I.105, B:Y.132, B:Y.132, B:L.213, B:A.243, B:I.244 Hydrogen bonds: B:Y.148 M1U.14: 10 residues within 4Å: Chain B: F.34, P.35, W.147, Y.148, L.170, M.173, S.177, V.242, H.270, W.271 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.34, B:W.147, B:Y.148, B:Y.148, B:L.170, B:M.173, B:W.271

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

CL.3: 5 residues within 4Å: Chain A: F.265, P.266, E.267, C.268 Ligands: EDO.11 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.6, H.7 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.251, M.252, E.253 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: D.292, I.293, H.294 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: H.7, H.18, W.38, N.63 Ligands: EDO.16 Ligand excluded by PLIP

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

EDO.7: 3 residues within 4Å: Chain A: V.10, K.11, K.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.11, A:K.16 Water bridges: A:K.11 EDO.8: 3 residues within 4Å: Chain A: P.68, E.69, N.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.69, A:N.73 EDO.9: 3 residues within 4Å: Chain A: R.75, A.211, N.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.212 Water bridges: A:L.76, A:N.214 EDO.10: 2 residues within 4Å: Chain A: H.7, W.38 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: Y.264, F.265, L.279 Ligands: CL.3 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain B: I.191 Ligands: CL.15 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.12: 2 residues within 4Å: Chain A: S.139, D.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.247 NA.17: 2 residues within 4Å: Chain B: S.139, D.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.139 Water bridges: B:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Isupov, M.N. et al., Complexes of epoxide hydrolase from metagenomic source ch65. To Be Published

Release Date

2023-08-16

Peptides

Alpha/beta epoxide hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Alpha/beta epoxide hydrolase

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