MolNFT v1 · #142379 · protein
Crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa
6A2F · Alanine racemase, biosynthetic: “Crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (DLY), 7 pockets (best druggability 0.74). MolNFT v1 #142379 on GenesisL1: 3D structure…
- PDB
- 6A2F
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase, biosynthetic
- EC
- 5.1.1.1
- UniProt
- Q9HUN4
- Ligands
- DLY
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase, biosynthetic (EC 5.1.1.1) | protein | 358 | 30% helix, 24% strand | Q9HUN4 |
Ligands and binding sites
- DLY · D-lysine · ligand · 2 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.74 | 0.88 | 60 | DLY, ACT, MLI |
| 2 | 268 | 0.74 | 0.87 | 67 | MLI, DLY, ACT |
| 3 | 72 | 0.59 | 0.89 | 21 | empty |
| 4 | 151 | 0.52 | 0.80 | 28 | empty |
| 5 | 151 | 0.49 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2860 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6A2F · Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HUN4 · AlphaFold monomer V2.0 prediction for alanine racemase, biosynthetic (Q9HUN4) · a predicted model of the same protein · 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 Q9HUN4
- Elsewhere: RCSB PDB 6A2F · PDBe 6A2F · UniProt Q9HUN4
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