Research workbench
Crystal structure of double mutant S12T and N87T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase from schistosoma mansoni in apo form
Analyse Crystal structure of double mutant S12T and N87T of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F7Z
- 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
- PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 285 | 31% helix, 25% strand | I0B503 |
| B | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 289 | 32% helix, 25% strand | I0B503 |
| C | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 287 | 31% helix, 24% strand | I0B503 |
| D | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 283 | 30% helix, 25% strand | I0B503 |
| E | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 279 | 30% helix, 25% strand | I0B503 |
| F | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 280 | 30% helix, 25% strand | I0B503 |
Ligands and binding sites
- PO4 · Phosphate 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.85 | 0.94 | 54 | empty |
| 2 | 353 | 0.85 | 0.94 | 54 | empty |
| 3 | 505 | 0.70 | 0.80 | 55 | PO4 |
| 4 | 581 | 0.70 | 0.79 | 71 | PO4 |
| 5 | 469 | 0.70 | 0.80 | 53 | PO4 |
Interfaces
7 interfaces between chains.
- B–D · 1193 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1190 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1138 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1121 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1118 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5F7Z · 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 5F7Z · PDBe 5F7Z · UniProt I0B503
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