MolNFT v1 · #91942 · protein
Complex structure of a broad specificity amino acid racemase (bar) within the reactive intermediate
4FS9: “Complex structure of a broad specificity amino acid racemase (bar) within the reactive intermediate”. X-ray diffraction, 1 ligand (PE1), 4 pockets (best druggability 0.77). MolNFT v1 #91942 on GenesisL1: 3D structure, binding sites…
- PDB
- 4FS9
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Broad specificity amino acid racemase
- EC
- 5.1.1.10
- Ligands
- PE1
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Broad specificity amino acid racemase (EC 5.1.1.10) | protein | 384 | 36% helix, 26% strand | — |
Ligands and binding sites
- PE1 · N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-lysine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.77 | 0.86 | 65 | PE1 |
| 2 | 325 | 0.76 | 0.87 | 55 | PE1 |
| 3 | 79 | 0.73 | 0.97 | 31 | empty |
| 4 | 61 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3546 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FS9 · Complex structure of a broad specificity amino acid racemase (Bar) within the reactive… · 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
- Elsewhere: RCSB PDB 4FS9 · PDBe 4FS9
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