MolNFT v1 · #21359 · protein
Structural basis for the mechanism and regulation of SIR2 enzymes
1S7G · NAD-dependent deacetylase 2: “Structural basis for the mechanism and regulation of SIR2 enzymes”. X-ray diffraction, 4 ligands (NAD, APR, ZN), 13 pockets (best druggability 0.83). MolNFT v1 #21359 on GenesisL1: 3D structure, binding…
- PDB
- 1S7G
- Type
- protein
- Length
- 1,244 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase 2
- EC
- 3.5.1.-
- UniProt
- O30124
- Ligands
- NAD, APR, ZN, SO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NAD-dependent deacetylase 2 (EC 3.5.1.-) | protein | 252 | 42% helix, 19% strand | O30124 |
| D | NAD-dependent deacetylase 2 (EC 3.5.1.-) | protein | 240 | 43% helix, 20% strand | O30124 |
| E | NAD-dependent deacetylase 2 (EC 3.5.1.-) | protein | 248 | 42% helix, 19% strand | O30124 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- APR · Adenosine-5-diphosphoribose · ligand · chains E
- ZN · Zinc ion · metal · 9 copies · chains A, C, B, D, E
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, D, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, D
- 1PE · Pentaethylene glycol · additive · chains A
- 2PE · Nonaethylene glycol · additive · chains B
- P6G · Hexaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.83 | 0.90 | 68 | NAD, 2PE |
| 2 | 579 | 0.80 | 0.86 | 59 | NAD, P6G |
| 3 | 708 | 0.80 | 0.84 | 61 | APR |
| 4 | 249 | 0.75 | 0.88 | 39 | 1PE, EDO |
| 5 | 410 | 0.74 | 0.84 | 56 | SO4 |
Interfaces
7 interfaces between chains.
- A–D · 888 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 814 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 332 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 105 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1S7G · Structural Basis for the Mechanism and Regulation of Sir2 Enzymes · the same entry in another collection · chain E against E, TM-score 1.00
- O30124 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase 2 (O30124) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 O30124
- Elsewhere: RCSB PDB 1S7G · PDBe 1S7G · UniProt O30124
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