MolNFT v1 · #113948 · protein
Crystal structure of mouse sahh complexed with 3'-keto aristeromycin
5AXC · Adenosylhomocysteinase: “Crystal structure of mouse sahh complexed with 3'-keto aristeromycin”. X-ray diffraction, 3 ligands (NAD, ARJ, NA), 8 pockets (best druggability 0.77). MolNFT v1 #113948 on GenesisL1: 3D structure, binding…
- PDB
- 5AXC
- Type
- protein
- Length
- 859 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P50247
- Ligands
- NAD, ARJ, NA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 429 | 45% helix, 16% strand | P50247 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 430 | 44% helix, 16% strand | P50247 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- ARJ · (2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-2-hydroxy-5-(hydroxymethyl)cyclopentanone · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.77 | 0.82 | 88 | NA |
| 2 | 452 | 0.71 | 0.81 | 68 | NAD, ARJ |
| 3 | 435 | 0.70 | 0.81 | 71 | NAD, ARJ |
| 4 | 260 | 0.56 | 0.77 | 33 | empty |
| 5 | 253 | 0.54 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–C · 1959 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5AXC · Crystal structure of mouse SAHH complexed with 3'-keto aristeromycin · the same entry in another collection · chain A against A, TM-score 1.00
- P50247 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P50247) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P50247
- Elsewhere: RCSB PDB 5AXC · PDBe 5AXC · UniProt P50247
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