MolNFT v1 · #163263 · protein
Crystal structure of cobb wt in complex with H4K16-butyryl peptide
6RXK · NAD-dependent protein deacylase: “Crystal structure of cobb wt in complex with H4K16-butyryl peptide”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.69). MolNFT v1 #163263 on GenesisL1: 3D structure, binding sites…
- PDB
- 6RXK
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase; Histone H4
- EC
- 3.5.1.-
- UniProt
- P75960, P02309
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 235 | 39% helix, 22% strand | P75960 |
| B | Histone H4 | protein | 9 | 0% helix, 22% strand | P02309 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.69 | 0.84 | 48 | empty |
| 2 | 59 | 0.34 | 0.77 | 12 | empty |
| 3 | 65 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 728 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6RXK · Crystal structure of CobB wt in complex with H4K16-Butyryl peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P75960 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase (P75960) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 P75960
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 6RXK · PDBe 6RXK · UniProt P75960 · UniProt P02309
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