MolNFT v1 · #104330 · protein
Crystal structure of N-acetyl-ORNITHINE/N-acetyl-lysine deacetylase from sphaerobacter thermophilus
4Q7A: “Crystal structure of N-acetyl-ORNITHINE/N-acetyl-lysine deacetylase from sphaerobacter thermophilus”. X-ray diffraction, 2 ligands (SO4, CL), 13 pockets (best druggability 0.71). MolNFT v1 #104330 on GenesisL1: 3D structure, binding…
- PDB
- 4Q7A
- Type
- protein
- Length
- 1,415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-ORNITHINE/N-acetyl-lysine deacetylase
- UniProt
- D1C6B5
- Ligands
- SO4, CL
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetyl-ORNITHINE/N-acetyl-lysine deacetylase | protein | 361 | 34% helix, 29% strand | D1C6B5 |
| C | N-acetyl-ORNITHINE/N-acetyl-lysine deacetylase | protein | 352 | 34% helix, 29% strand | D1C6B5 |
| D | N-acetyl-ORNITHINE/N-acetyl-lysine deacetylase | protein | 341 | 34% helix, 28% strand | D1C6B5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.71 | 0.79 | 83 | empty |
| 2 | 648 | 0.70 | 0.78 | 73 | empty |
| 3 | 671 | 0.66 | 0.76 | 76 | SO4 |
| 4 | 172 | 0.54 | 0.80 | 24 | empty |
| 5 | 157 | 0.54 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1345 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1343 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1244 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4Q7A · Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter… · 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 D1C6B5
- Elsewhere: RCSB PDB 4Q7A · PDBe 4Q7A · UniProt D1C6B5
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