Research workbench
Crystal structure of mutant N87T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase from schistosoma mansoni in apo form
Analyse Crystal structure of mutant N87T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F78
- Type
- protein
- Length
- 1,721 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
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 289 | 32% helix, 23% strand | I0B503 |
| C | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 287 | 32% helix, 25% strand | I0B503 |
| D | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 33% helix, 24% strand | I0B503 |
| E | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 288 | 32% helix, 25% strand | I0B503 |
| F | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 282 | 30% helix, 25% strand | I0B503 |
Ligands and binding sites
- 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.86 | 0.93 | 62 | empty |
| 2 | 386 | 0.85 | 0.93 | 50 | empty |
| 3 | 758 | 0.76 | 0.81 | 83 | SO4 |
| 4 | 558 | 0.74 | 0.82 | 56 | SO4 |
| 5 | 528 | 0.74 | 0.82 | 53 | SO4 |
Interfaces
7 interfaces between chains.
- A–C · 1223 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1204 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1191 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1185 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5F78 · Crystal structure of Mutant N87T of adenosine/Methylthioadenosine phosphorylase from… · the same entry in another collection · chain C against C, 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 5F78 · PDBe 5F78 · UniProt I0B503
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