Research workbench
Methylthioadenosine phosphorylase from schistosoma mansoni in complex with adenine
Analyse Methylthioadenosine phosphorylase from schistosoma mansoni in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L6I
- Type
- protein
- Length
- 1,718 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-methyl-5'-thioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- I0B503
- Ligands
- ADE, SO4
- 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 | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 289 | 30% helix, 25% strand | I0B503 |
| B | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 290 | 30% helix, 25% strand | I0B503 |
| C | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 277 | 33% helix, 25% strand | I0B503 |
| D | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 31% helix, 26% strand | I0B503 |
| E | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 288 | 31% helix, 25% strand | I0B503 |
| F | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 288 | 31% helix, 25% strand | I0B503 |
Ligands and binding sites
- ADE · Adenine · ligand · 4 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, 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 | 399 | 0.85 | 0.94 | 57 | empty |
| 2 | 390 | 0.85 | 0.94 | 52 | empty |
| 3 | 511 | 0.77 | 0.84 | 61 | ADE |
| 4 | 89 | 0.76 | 0.98 | 26 | ADE, SO4 |
| 5 | 80 | 0.76 | 0.98 | 26 | ADE, SO4 |
Interfaces
7 interfaces between chains.
- D–F · 1418 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1312 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1304 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1255 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1125 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4L6I · Methylthioadenosine phosphorylase from Schistosoma mansoni in complex with adenine · 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 4L6I · PDBe 4L6I · UniProt I0B503
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