MolNFT v1 · #120745 · protein
Structure of a diaminopimelate epimerase from acinetobacter baumannii
5HA4: “Structure of a diaminopimelate epimerase from acinetobacter baumannii”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.59). MolNFT v1 #120745 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HA4
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase
- EC
- 5.1.1.7
- UniProt
- B7GY71
- Ligands
- CL
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 280 | 19% helix, 37% strand | B7GY71 |
| B | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 282 | 18% helix, 38% strand | B7GY71 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.59 | 0.79 | 24 | MRD |
| 2 | 249 | 0.56 | 0.77 | 27 | empty |
| 3 | 114 | 0.44 | 0.78 | 20 | empty |
| 4 | 88 | 0.41 | 0.78 | 20 | empty |
| 5 | 60 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 971 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5HA4 · Structure of a diaminopimelate epimerase from Acinetobacter baumannii · the same entry in another collection · chain A against A, TM-score 1.00
- B7GY71 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (B7GY71) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B7GY71
- Elsewhere: RCSB PDB 5HA4 · PDBe 5HA4 · UniProt B7GY71
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