MolNFT v1 · #110644 · protein
Crystal structure of a thermostable alanine racemase from thermoanaerobacter tengcongensis MB4
4Y2W · Alanine racemase 1: “Crystal structure of a thermostable alanine racemase from thermoanaerobacter tengcongensis MB4”. X-ray diffraction, 2 ligands (ALA, PO4), 10 pockets (best druggability 0.81). MolNFT v1 #110644 on GenesisL1: 3D…
- PDB
- 4Y2W
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase 1
- EC
- 5.1.1.1
- UniProt
- Q8RAK6
- Ligands
- ALA, PO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase 1 (EC 5.1.1.1) | protein | 388 | 34% helix, 26% strand | Q8RAK6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.81 | 0.90 | 63 | ALA, PO4 |
| 2 | 129 | 0.79 | 0.98 | 40 | empty |
| 3 | 283 | 0.76 | 0.88 | 45 | PO4, ALA |
| 4 | 52 | 0.67 | 0.96 | 19 | empty |
| 5 | 282 | 0.54 | 0.76 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 3219 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 4Y2W · Crystal structure of a thermostable alanine racemase from Thermoanaerobacter… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8RAK6 · AlphaFold monomer V2.0 prediction for alanine racemase 1 (Q8RAK6) · 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 Q8RAK6
- Elsewhere: RCSB PDB 4Y2W · PDBe 4Y2W · UniProt Q8RAK6
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