MolNFT v1 · #163268 · protein
Crystal structure of cobb AC2 (A76G,I131C,V162A) in complex with H4K16-crotonyl peptide
6RXP · NAD-dependent protein deacylase: “Crystal structure of cobb AC2 (A76G,I131C,V162A) in complex with H4K16-crotonyl peptide”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.74). MolNFT v1 #163268 on GenesisL1: 3D…
- PDB
- 6RXP
- Type
- protein
- Length
- 489 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
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 233 | 36% helix, 22% strand | P75960 |
| B | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 235 | 38% helix, 23% strand | P75960 |
| C | Histone H4 | protein | 10 | 0% helix, 20% strand | P02309 |
| D | Histone H4 | protein | 11 | 0% helix, 18% 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.74 | 0.90 | 31 | empty |
| 2 | 318 | 0.72 | 0.84 | 43 | empty |
| 3 | 66 | 0.67 | 0.94 | 25 | empty |
| 4 | 298 | 0.50 | 0.73 | 35 | empty |
| 5 | 162 | 0.44 | 0.75 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–D · 743 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 411 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 323 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6RXP · Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.29
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 6RXP · PDBe 6RXP · UniProt P75960 · UniProt P02309
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