MolNFT v1 · #141899 · protein
Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)- tartaric acids
5ZMU: “Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)- tartaric acids”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.66). MolNFT v1 #141899 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZMU
- Type
- protein
- Length
- 1,129 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cis-epoxysuccinate hydrolase
- UniProt
- F1LJ99
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cis-epoxysuccinate hydrolase | protein | 281 | 36% helix, 19% strand | F1LJ99 |
| C | Cis-epoxysuccinate hydrolase | protein | 280 | 36% helix, 19% strand | F1LJ99 |
| D | Cis-epoxysuccinate hydrolase | protein | 287 | 36% helix, 20% strand | F1LJ99 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.66 | 0.76 | 70 | empty |
| 2 | 344 | 0.62 | 0.78 | 32 | empty |
| 3 | 311 | 0.60 | 0.78 | 33 | ZN |
| 4 | 312 | 0.60 | 0.78 | 35 | ZN |
| 5 | 50 | 0.36 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1769 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1766 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 172 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ZMU · Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)-tartaric acids · 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 F1LJ99
- Elsewhere: RCSB PDB 5ZMU · PDBe 5ZMU · UniProt F1LJ99
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