MolNFT v1 · #118720 · protein
Crystal structure of double mutant S12T and N87T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase from schistosoma mansoni in complex with adenine
5FAK: “Crystal structure of double mutant S12T and N87T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase from…”. X-ray diffraction, 2 ligands (ADE, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #118720 on GenesisL1: 3D structure…
- PDB
- 5FAK
- Type
- protein
- Length
- 1,703 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylthioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- I0B503
- Ligands
- ADE, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 283 | 32% helix, 27% strand | I0B503 |
| B | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 30% helix, 26% strand | I0B503 |
| C | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 31% helix, 26% strand | I0B503 |
| D | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 282 | 31% helix, 26% strand | I0B503 |
| E | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 283 | 30% helix, 26% strand | I0B503 |
| F | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 283 | 30% helix, 26% strand | I0B503 |
Ligands and binding sites
- ADE · Adenine · ligand · 4 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.84 | 0.93 | 51 | empty |
| 2 | 403 | 0.83 | 0.91 | 51 | empty |
| 3 | 97 | 0.78 | 0.98 | 25 | ADE, SO4 |
| 4 | 103 | 0.78 | 0.98 | 27 | ADE, SO4 |
| 5 | 132 | 0.78 | 0.96 | 28 | ADE, SO4 |
Interfaces
8 interfaces between chains.
- A–C · 1293 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1217 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1186 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1095 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1062 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5FAK · Crystal structure of Double Mutant S12T and N87T of Adenosine/Methylthioadenosine… · 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 5FAK · PDBe 5FAK · UniProt I0B503
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