Research workbench
X-ray structure of the haloalcohol dehalogenase hhec of agrobacterium radiobacter AD1 in complex with (S)-para- nitrostyrene oxide, with a water molecule in the halide- binding site
Analyse X-ray structure of the haloalcohol dehalogenase hhec of agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZO8
- Type
- protein
- Length
- 4,032 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halohydrin dehalogenase
- EC
- 4.5.-.-
- UniProt
- Q7AUG5
- Ligands
- SNO
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Halohydrin dehalogenase (EC 4.5.-.-) | protein | 252 | 48% helix, 14% strand | Q7AUG5 |
Ligands and binding sites
- SNO · (S)-para-nitrostyrene oxide · ligand · 16 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, N, O, P
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 | 968 | 0.86 | 0.88 | 124 | SNO |
| 2 | 959 | 0.86 | 0.87 | 95 | empty |
| 3 | 1177 | 0.85 | 0.86 | 94 | empty |
| 4 | 1161 | 0.85 | 0.86 | 92 | empty |
| 5 | 801 | 0.84 | 0.87 | 112 | SNO |
Interfaces
34 interfaces between chains.
- A–B · 1706 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1704 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1701 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 1699 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1677 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1ZO8 · X-ray Structure of the haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in… · the same entry in another collection · chain A against A, 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
- Every structure of UniProt Q7AUG5
- Elsewhere: RCSB PDB 1ZO8 · PDBe 1ZO8 · UniProt Q7AUG5
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