MolNFT v1 · #163262 · protein
Crystal structure of cobb wt in complex with H4K16-acetyl peptide
6RXJ · NAD-dependent protein deacylase: “Crystal structure of cobb wt in complex with H4K16-acetyl peptide”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.72). MolNFT v1 #163262 on GenesisL1: 3D structure, binding sites…
- PDB
- 6RXJ
- Type
- protein
- Length
- 485 residues
- Chains
- 4
- 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
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 235 | 39% helix, 22% strand | P75960 |
| C | Histone H4 | protein | 7 | 0% helix, 29% strand | P02309 |
| D | Histone H4 | protein | 8 | 0% helix, 25% strand | P02309 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.72 | 0.84 | 51 | empty |
| 2 | 330 | 0.70 | 0.83 | 42 | empty |
| 3 | 222 | 0.55 | 0.78 | 30 | empty |
| 4 | 95 | 0.35 | 0.74 | 16 | empty |
| 5 | 52 | 0.34 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–D · 653 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 568 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 6RXJ · Crystal structure of CobB wt in complex with H4K16-Acetyl 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 D against A, TM-score 0.35
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 6RXJ · PDBe 6RXJ · UniProt P75960 · UniProt P02309
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