Research workbench
Crystal structure of Escherichia coli alaine racemase mutant P219A
Analyse Crystal structure of Escherichia coli alaine racemase mutant P219A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8T
- Type
- protein
- Length
- 1,419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Escherichia coli
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- P0A6B4
- Ligands
- PLP, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 3 · 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 | 350 | 30% helix, 23% strand | P0A6B4 |
| D | Alanine racemase (EC 5.1.1.1) | protein | 351 | 29% helix, 25% strand | P0A6B4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.80 | 0.90 | 59 | SO4, PLP |
| 2 | 368 | 0.79 | 0.88 | 58 | PLP |
| 3 | 410 | 0.77 | 0.86 | 64 | PLP |
| 4 | 346 | 0.76 | 0.87 | 52 | PLP |
| 5 | 388 | 0.71 | 0.83 | 50 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2932 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2885 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified (pyridoxal phosphate Schiff base, carboxylation).
Compared structures
- 3B8T · Crystal structure of escherichia COLI alaine racemase mutant P219A · 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 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 P0A6B4
- Elsewhere: RCSB PDB 3B8T · PDBe 3B8T · UniProt P0A6B4
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