Research workbench
Crystal structure of biosynthetic alaine racemase in D- cycloserine-bound form from escherichia COLI
Analyse Crystal structure of biosynthetic alaine racemase in D- cycloserine-bound form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RJH
- Type
- protein
- Length
- 1,428 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
- DCS, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% 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 | 353 | 29% helix, 26% strand | P0A6B4 |
| D | Alanine racemase (EC 5.1.1.1) | protein | 357 | 31% helix, 26% strand | P0A6B4 |
Ligands and binding sites
- DCS · D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.82 | 0.93 | 42 | DCS |
| 2 | 341 | 0.81 | 0.91 | 56 | DCS |
| 3 | 358 | 0.81 | 0.90 | 58 | DCS |
| 4 | 412 | 0.80 | 0.89 | 67 | DCS |
| 5 | 378 | 0.70 | 0.82 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2962 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2828 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 2RJH · Crystal structure of biosynthetic alaine racemase in D-cycloserine-bound form from… · 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 2RJH · PDBe 2RJH · UniProt P0A6B4
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