MolNFT v1 · #38673 · protein
S-adenosylhomocysteine hydrolase containing NAD and 3-deaza-D- eritadenine
2H5L · Adenosylhomocysteinase: “S-adenosylhomocysteine hydrolase containing NAD and 3-deaza-D- eritadenine”. X-ray diffraction, 2 ligands (NAD, 3DD), 20 pockets (best druggability 0.89). MolNFT v1 #38673 on GenesisL1: 3D structure, binding…
- PDB
- 2H5L
- Type
- protein
- Length
- 3,440 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P10760
- Ligands
- NAD, 3DD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 430 | 45% helix, 16% strand | P10760 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 3DD · (2R,3R)-4-(4-amino-1H-imidazo[4,5-c]pyridin-1-yl)-2,3-dihydroxybutanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.89 | 0.91 | 69 | empty |
| 2 | 931 | 0.89 | 0.91 | 73 | empty |
| 3 | 1153 | 0.85 | 0.86 | 126 | NAD, 3DD |
| 4 | 664 | 0.85 | 0.89 | 79 | NAD, 3DD |
| 5 | 715 | 0.84 | 0.88 | 84 | NAD, 3DD |
Interfaces
15 interfaces between chains.
- A–B · 3186 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 3166 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 3163 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3151 Ų buried · 36 hydrogen bonds · protein-protein
- E–G · 1865 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2H5L · S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine · the same entry in another collection · chain H against H, TM-score 1.00
- P10760 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P10760) · a predicted model of the same protein · chain A against A, 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 P10760
- Elsewhere: RCSB PDB 2H5L · PDBe 2H5L · UniProt P10760
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