MolNFT v1 · #163265 · protein
Crystal structure of cobb AC2 (A76G, I131C, V162G) in complex with H4K16-acetyl peptide
6RXM · NAD-dependent protein deacylase: “Crystal structure of cobb AC2 (A76G, I131C, V162G) in complex with H4K16-acetyl peptide”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.82). MolNFT v1 #163265 on GenesisL1: 3D…
- PDB
- 6RXM
- Type
- protein
- Length
- 1,446 residues
- Chains
- 12
- 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
- 17 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 235 | 36% helix, 22% strand | P75960 |
| B | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 234 | 36% helix, 22% strand | P75960 |
| D | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 227 | 38% helix, 21% strand | P75960 |
| E, F | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 233 | 39% helix, 22% strand | P75960 |
| G, H, I | Histone H4 | protein | 7 | 0% helix, 29% strand | P02309 |
| J | Histone H4 | protein | 8 | 0% helix, 25% strand | P02309 |
| K | Histone H4 | protein | 9 | 0% helix, 22% strand | P02309 |
| L | Histone H4 | protein | 11 | 0% helix, 18% strand | P02309 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.82 | 0.89 | 66 | empty |
| 2 | 1088 | 0.80 | 0.81 | 107 | empty |
| 3 | 654 | 0.77 | 0.82 | 87 | empty |
| 4 | 535 | 0.76 | 0.83 | 69 | empty |
| 5 | 977 | 0.74 | 0.77 | 99 | empty |
Interfaces
26 interfaces between chains.
- E–K · 669 Ų buried · 10 hydrogen bonds · protein-protein
- F–L · 625 Ų buried · 8 hydrogen bonds · protein-protein
- C–I · 624 Ų buried · 8 hydrogen bonds · protein-protein
- D–J · 616 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (acetylation).
Compared structures
- 6RXM · Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide · the same entry in another collection · chain L against L, 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 P75960
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 6RXM · PDBe 6RXM · UniProt P75960 · UniProt P02309
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