Research workbench
Structure of haloalcohol dehalogenase hhec of agrobacterium radiobacter AD1 in complex with (R)-para-nitro styrene oxide, with a water molecule in the halide-binding site
Analyse Structure of haloalcohol dehalogenase hhec of agrobacterium radiobacter AD1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZMT
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalcohol dehalogenase hhec
- UniProt
- Q93D82
- Ligands
- RNO
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Haloalcohol dehalogenase hhec | protein | 252 | 48% helix, 13% strand | Q93D82 |
Ligands and binding sites
- RNO · (R)-para-nitrostyrene oxide · ligand · 4 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.85 | 0.86 | 92 | empty |
| 2 | 87 | 0.59 | 0.87 | 21 | RNO |
| 3 | 80 | 0.58 | 0.87 | 19 | RNO |
| 4 | 79 | 0.55 | 0.86 | 19 | RNO |
| 5 | 168 | 0.54 | 0.79 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1705 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1668 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1480 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1476 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1174 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1ZMT · Structure of haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex… · 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 Q93D82
- Elsewhere: RCSB PDB 1ZMT · PDBe 1ZMT · UniProt Q93D82
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