Research workbench
Crystal structure of oxidized dapf from corynebacterium glutamicum
Analyse Crystal structure of oxidized dapf from corynebacterium glutamicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H2G
- Type
- protein
- Length
- 558 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
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 278 | 15% helix, 46% strand | Q8NP73 |
| B | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 280 | 15% helix, 46% strand | Q8NP73 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.60 | 0.79 | 34 | GOL |
| 2 | 146 | 0.48 | 0.78 | 27 | empty |
| 3 | 81 | 0.35 | 0.75 | 16 | empty |
| 4 | 64 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 894 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5H2G · Crystal structure of oxidized 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 A 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 5H2G · PDBe 5H2G · UniProt Q8NP73
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