MolNFT v1 · #120521 · protein
Crystal structure of reduced dapf from corynebacterium glutamicum
5H2Y · Diaminopimelate epimerase: “Crystal structure of reduced dapf from corynebacterium glutamicum”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #120521 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H2Y
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase
- EC
- 5.1.1.7
- UniProt
- Q8NP73
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 278 | 16% helix, 45% strand | Q8NP73 |
| B | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 276 | 15% helix, 45% strand | Q8NP73 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.58 | 0.78 | 32 | empty |
| 2 | 245 | 0.57 | 0.79 | 26 | empty |
| 3 | 78 | 0.35 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 901 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5H2Y · Crystal structure of reduced DapF from Corynebacterium glutamicum · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NP73 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (Q8NP73) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8NP73
- Elsewhere: RCSB PDB 5H2Y · PDBe 5H2Y · UniProt Q8NP73
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