MolNFT v1 · #111596 · protein
Structure of S-adenosyl-L-homocysteine hydrolase
4YVF · Adenosylhomocysteinase: “Structure of S-adenosyl-L-homocysteine hydrolase”. X-ray diffraction, 2 ligands (NAI, XFA), 6 pockets (best druggability 0.80). MolNFT v1 #111596 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YVF
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P23526
- Ligands
- NAI, XFA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 429 | 45% helix, 17% strand | P23526 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- XFA · 2-{[5-chloro-2-(4-chlorophenoxy)phenyl](2-{[2-(methylamino)ethyl]amino}-2-oxoethyl)amino}-N-(1,3-dihydro-2H-isoindol-2-yl)-N-methylacetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.80 | 0.90 | 29 | empty |
| 2 | 1097 | 0.79 | 0.80 | 85 | NAI, XFA |
| 3 | 1104 | 0.78 | 0.80 | 90 | NAI, XFA |
| 4 | 151 | 0.52 | 0.79 | 27 | empty |
| 5 | 109 | 0.39 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2934 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
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 P23526
- Elsewhere: RCSB PDB 4YVF · PDBe 4YVF · UniProt P23526
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