MolNFT v1 · #28364 · protein

SIR2AF2-NAD-adpribose-nicotinamide

1YC2 · NAD-dependent deacetylase 2: “SIR2AF2-NAD-adpribose-nicotinamide”. X-ray diffraction, 5 ligands (NCA, NAD, APR), 13 pockets (best druggability 0.85). MolNFT v1 #28364 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YC2
Type: protein
Length: 1,257 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: NCA, NAD, APR, ZN, SO4
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	NAD-dependent deacetylase 2 (EC 3.5.1.-)	protein	252	44% helix, 19% strand	O30124
D	NAD-dependent deacetylase 2 (EC 3.5.1.-)	protein	251	42% helix, 19% strand	O30124
E	NAD-dependent deacetylase 2 (EC 3.5.1.-)	protein	250	42% helix, 18% strand	O30124

Ligands and binding sites

NCA · Nicotinamide · ligand · 5 copies · chains A, B, C, D, E
NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
APR · Adenosine-5-diphosphoribose · ligand · chains E
ZN · Zinc ion · metal · 9 copies · chains A, C, B, D, E
SO4 · Sulfate ion · ion · 10 copies · chains A, D, B, C
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
2PE · Nonaethylene glycol · additive · 2 copies · chains B, C
PG4 · Tetraethylene glycol · additive · chains D
PGE · Triethylene glycol · additive · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	658	0.85	0.89	78	NAD, NCA, EDO
2	463	0.83	0.90	58	NAD, 2PE, NCA
3	1122	0.82	0.83	99	NAD, NCA, PG4, PGE
4	457	0.81	0.88	55	APR, NCA
5	448	0.80	0.87	46	NAD, 2PE

Interfaces

7 interfaces between chains.

A–C · 934 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 878 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 861 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 328 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 99 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1YC2 · Sir2Af2-NAD-ADPribose-nicotinamide · 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 1YC2 · PDBe 1YC2 · UniProt O30124

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