MolNFT v1 · #109733 · protein
Y274F alanine racemase from E. COLI inhibited by L-ala-P
4XBJ · Alanine racemase, biosynthetic: “Y274F alanine racemase from E. COLI inhibited by L-ala-P”. X-ray diffraction, 2 ligands (IN5, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #109733 on GenesisL1: 3D structure, binding sites…
- PDB
- 4XBJ
- Type
- protein
- Length
- 1,417 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase, biosynthetic
- EC
- 5.1.1.1
- UniProt
- P0A6B4
- Ligands
- IN5, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase, biosynthetic (EC 5.1.1.1) | protein | 357 | 31% helix, 24% strand | P0A6B4 |
| B | Alanine racemase, biosynthetic (EC 5.1.1.1) | protein | 358 | 31% helix, 24% strand | P0A6B4 |
| C | Alanine racemase, biosynthetic (EC 5.1.1.1) | protein | 351 | 29% helix, 24% strand | P0A6B4 |
| D | Alanine racemase, biosynthetic (EC 5.1.1.1) | protein | 351 | 30% helix, 26% strand | P0A6B4 |
Ligands and binding sites
- IN5 · {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid · ligand · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.82 | 0.91 | 58 | IN5, SO4 |
| 2 | 422 | 0.81 | 0.89 | 69 | IN5, SO4 |
| 3 | 411 | 0.79 | 0.87 | 61 | SO4 |
| 4 | 421 | 0.78 | 0.87 | 67 | IN5, SO4 |
| 5 | 351 | 0.72 | 0.84 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2904 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2744 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 1 hydrogen bond · protein-protein
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 P0A6B4
- Elsewhere: RCSB PDB 4XBJ · PDBe 4XBJ · UniProt P0A6B4
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