MolNFT v1 · #163267 · protein
Crystal structure of cobb AC2 (A76G, I131C, V162A) in complex with H4K16-buturyl peptide
6RXO · NAD-dependent protein deacylase: “Crystal structure of cobb AC2 (A76G, I131C, V162A) in complex with H4K16-buturyl peptide”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.77). MolNFT v1 #163267 on GenesisL1: 3D…
- PDB
- 6RXO
- Type
- protein
- Length
- 488 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 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 235 | 39% helix, 21% strand | P75960 |
| C | Histone H4 | protein | 10 | 0% helix, 20% 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 | 603 | 0.77 | 0.83 | 65 | empty |
| 2 | 362 | 0.71 | 0.83 | 42 | empty |
| 3 | 239 | 0.51 | 0.75 | 35 | empty |
| 4 | 244 | 0.49 | 0.74 | 35 | empty |
| 5 | 55 | 0.33 | 0.77 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–C · 599 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 593 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 385 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 264 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 183 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6RXO · Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl 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 0.98
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain D against A, TM-score 0.45
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 6RXO · PDBe 6RXO · UniProt P75960 · UniProt P02309
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