Research workbench
Crystal structure of pseudomonas fluorescens alanine racemase
Analyse Crystal structure of pseudomonas fluorescens alanine racemase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ODO
- Type
- protein
- Length
- 1,424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q4ADX2
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alanine racemase (EC 5.1.1.1) | protein | 356 | 31% helix, 23% strand | Q4ADX2 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.67 | 0.82 | 55 | ACT |
| 2 | 222 | 0.66 | 0.84 | 38 | ACT |
| 3 | 307 | 0.65 | 0.81 | 47 | ACT |
| 4 | 205 | 0.62 | 0.83 | 36 | ACT |
| 5 | 235 | 0.53 | 0.77 | 39 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3033 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3026 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation, cofactor).
Compared structures
- 2ODO · Crystal structure of Pseudomonas Fluorescens alanine racemase · the same entry in another collection · 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 Q4ADX2
- Elsewhere: RCSB PDB 2ODO · PDBe 2ODO · UniProt Q4ADX2
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