MolNFT v1 · #28194 · protein
Cyrstal structure of MTA/ADOHCY nucleosidase complexed with mt-dadme-imma
1Y6Q · MTA/SAH nucleosidase: “Cyrstal structure of MTA/ADOHCY nucleosidase complexed with mt-dadme-imma”. X-ray diffraction, 2 ligands (TDI, CL), 5 pockets (best druggability 0.73). MolNFT v1 #28194 on GenesisL1: 3D structure, binding…
- PDB
- 1Y6Q
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MTA/SAH nucleosidase
- EC
- 3.2.2.16, 3.2.2.9
- UniProt
- P24247
- Ligands
- TDI, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9) | protein | 234 | 38% helix, 30% strand | P24247 |
| B | MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9) | protein | 232 | 39% helix, 31% strand | P24247 |
Ligands and binding sites
- TDI · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.73 | 0.92 | 25 | TDI |
| 2 | 120 | 0.73 | 0.93 | 23 | TDI |
| 3 | 321 | 0.65 | 0.81 | 40 | empty |
| 4 | 55 | 0.34 | 0.78 | 15 | empty |
| 5 | 54 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1442 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1Y6Q · Cyrstal structure of MTA/AdoHcy nucleosidase complexed with MT-DADMe-ImmA · the same entry in another collection · 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 P24247
- Elsewhere: RCSB PDB 1Y6Q · PDBe 1Y6Q · UniProt P24247
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