MolNFT v1 · #118605 · protein
Crystal structure of mutant S12T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase from schistosoma mansoni in complex with methylthioadenosine
5F76: “Crystal structure of mutant S12T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase from schistosoma mansoni in…”. X-ray diffraction, 2 ligands (MTA, SO4), 13 pockets (best druggability 0.85). MolNFT v1 #118605 on GenesisL1: 3D…
- PDB
- 5F76
- Type
- protein
- Length
- 859 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylthioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- I0B503
- Ligands
- MTA, SO4
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 31% helix, 26% strand | I0B503 |
| B | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 289 | 31% helix, 25% strand | I0B503 |
| C | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 284 | 31% helix, 26% strand | I0B503 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.85 | 0.94 | 61 | empty |
| 2 | 126 | 0.81 | 0.99 | 27 | MTA, SO4 |
| 3 | 132 | 0.81 | 0.98 | 27 | MTA, SO4 |
| 4 | 420 | 0.68 | 0.80 | 45 | MTA, SO4 |
| 5 | 374 | 0.61 | 0.77 | 63 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1269 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1228 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1069 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5F76 · Crystal structure of Mutant S12T of Adenosine/Methylthioadenosine Phosphorylase from… · 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 I0B503
- Elsewhere: RCSB PDB 5F76 · PDBe 5F76 · UniProt I0B503
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