MolNFT v1 · #58612 · protein
Crystal structure of escherichia COLI alaine racemase mutant E221P
3B8W · Alanine racemase: “Crystal structure of escherichia COLI alaine racemase mutant E221P”. X-ray diffraction, 2 ligands (PLP, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #58612 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3B8W
- Type
- protein
- Length
- 1,418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- P0A6B4
- Ligands
- PLP, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase (EC 5.1.1.1) | protein | 359 | 31% helix, 24% strand | P0A6B4 |
| C | Alanine racemase (EC 5.1.1.1) | protein | 347 | 29% helix, 23% strand | P0A6B4 |
| D | Alanine racemase (EC 5.1.1.1) | protein | 353 | 29% helix, 24% strand | P0A6B4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.78 | 0.88 | 60 | PLP |
| 2 | 365 | 0.77 | 0.87 | 58 | PLP, SO4 |
| 3 | 389 | 0.76 | 0.86 | 62 | PLP |
| 4 | 380 | 0.76 | 0.86 | 61 | PLP |
| 5 | 333 | 0.71 | 0.84 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2934 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2738 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified (pyridoxal phosphate Schiff base, carboxylation).
Compared structures
- 3B8W · Crystal structure of Escherichia coli alaine racemase mutant E221P · the same entry in another collection · chain D against D, TM-score 1.00
- P0A6B4 · AlphaFold monomer V2.0 prediction for alanine racemase, biosynthetic (P0A6B4) · a predicted model of the same protein · chain C 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 P0A6B4
- Elsewhere: RCSB PDB 3B8W · PDBe 3B8W · UniProt P0A6B4
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