MolNFT v1 · #13276 · protein
Alanine racemase bound with N-(5'-phosphopyridoxyl)-D- alanine
1L6G: “Alanine racemase bound with N-(5'-phosphopyridoxyl)-D- alanine”. X-ray diffraction, 1 ligand (PDD), 9 pockets (best druggability 0.76). MolNFT v1 #13276 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1L6G
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- P10724
- Ligands
- PDD
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase (EC 5.1.1.1) | protein | 382 | 33% helix, 27% strand | P10724 |
Ligands and binding sites
- PDD · N-(5'-phosphopyridoxyl)-D-alanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.76 | 0.90 | 49 | PDD |
| 2 | 234 | 0.76 | 0.90 | 54 | PDD |
| 3 | 437 | 0.72 | 0.82 | 72 | empty |
| 4 | 94 | 0.53 | 0.84 | 21 | empty |
| 5 | 99 | 0.51 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3336 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
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 P10724
- Elsewhere: RCSB PDB 1L6G · PDBe 1L6G · UniProt P10724
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