Research workbench
Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. CH55-sample-peg complex
Analyse Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AII
- Type
- protein
- Length
- 2,011 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Limonene-1,2-epoxide hydrolase
- EC
- 3.3.2.8
- Ligands
- HIS
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, G, I, J, K, L, M, O | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 125 | 27% helix, 47% strand | — |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 127 | 28% helix, 46% strand | — |
| C, P | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 126 | 28% helix, 47% strand | — |
| F | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 124 | 28% helix, 48% strand | — |
| H, N | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 129 | 28% helix, 46% strand | — |
Ligands and binding sites
- HIS · Histidine · ligand · chains F
- PG4 · Tetraethylene glycol · additive · 24 copies · chains A, B, C, D, L, O, P, E, F, G, H, I, J, K, M, N
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, C, D, L, F, G, H, K, M, N, P, J
- PEG · Di(hydroxyethyl)ether · additive · 16 copies · chains A, B, M, D, F, E, H, I, J, K, L, O
- ACT · Acetate ion · additive · 11 copies · chains A, B, M, C, D, L, G, H, I, J, K, N, P, O
- PGE · Triethylene glycol · additive · 6 copies · chains C, D, P, I, K, L, H, M, N
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains I, J, N
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.83 | 0.86 | 77 | PG4, PEG |
| 2 | 719 | 0.82 | 0.85 | 74 | PG4 |
| 3 | 247 | 0.78 | 0.91 | 37 | PG4, EDO |
| 4 | 272 | 0.77 | 0.89 | 44 | ACT, PG4 |
| 5 | 967 | 0.76 | 0.79 | 85 | ACT, PGE, PG4 |
Interfaces
34 interfaces between chains.
- M–N · 915 Ų buried · 15 hydrogen bonds · protein-protein
- O–P · 914 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 913 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 911 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 910 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5AII · Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot… · the same entry in another collection · chain E against E, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5AII · PDBe 5AII
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