MolNFT v1 · #112171 · protein
Halohydrin hydrogen-halide-lyase, hheb
4ZD6 · Halohydrin epoxidase B: “Halohydrin hydrogen-halide-lyase, hheb”. X-ray diffraction, 2 ligands (MG, CL), 8 pockets (best druggability 0.86). MolNFT v1 #112171 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZD6
- Type
- protein
- Length
- 1,347 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halohydrin epoxidase B
- UniProt
- Q46347
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Halohydrin epoxidase B | protein | 225 | 44% helix, 16% strand | Q46347 |
| C, D, E | Halohydrin epoxidase B | protein | 224 | 45% helix, 17% strand | Q46347 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, A, E
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.86 | 0.92 | 48 | empty |
| 2 | 943 | 0.80 | 0.82 | 102 | MG |
| 3 | 517 | 0.76 | 0.84 | 52 | empty |
| 4 | 356 | 0.65 | 0.79 | 39 | empty |
| 5 | 320 | 0.64 | 0.80 | 34 | MES |
Interfaces
9 interfaces between chains.
- E–F · 1671 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1665 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1633 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1481 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4ZD6 · Halohydrin hydrogen-halide-lyase, HheB · 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 Q46347
- Elsewhere: RCSB PDB 4ZD6 · PDBe 4ZD6 · UniProt Q46347
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