MolNFT v1 · #98299 · protein
Methylthioadenosine phosphorylase from schistosoma mansoni in complex with tubercidin
4L5A · S-methyl-5'-thioadenosine phosphorylase: “Methylthioadenosine phosphorylase from schistosoma mansoni in complex with tubercidin”. X-ray diffraction, 2 ligands (TBN, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #98299 on…
- PDB
- 4L5A
- Type
- protein
- Length
- 1,689 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
- TBN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 282 | 30% helix, 25% strand | I0B503 |
| B | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 279 | 29% helix, 26% strand | I0B503 |
| C | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 284 | 30% helix, 26% strand | I0B503 |
| D | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 283 | 31% helix, 25% strand | I0B503 |
| E | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 279 | 29% helix, 26% strand | I0B503 |
| F | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 282 | 28% helix, 26% strand | I0B503 |
Ligands and binding sites
- TBN · 2-(4-amino-pyrrolo[2,3-d]pyrimidin-7-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · 6 copies · chains A, C, B, D, F, 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 | 341 | 0.84 | 0.94 | 55 | empty |
| 2 | 365 | 0.84 | 0.93 | 52 | empty |
| 3 | 116 | 0.78 | 0.97 | 26 | TBN, SO4 |
| 4 | 339 | 0.65 | 0.80 | 37 | TBN, SO4 |
| 5 | 372 | 0.65 | 0.79 | 46 | TBN, SO4 |
Interfaces
7 interfaces between chains.
- A–C · 1239 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1098 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1084 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1071 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1059 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4L5A · Methylthioadenosine phosphorylase from Schistosoma mansoni in complex with tubercidin · the same entry in another collection · chain E against E, 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 4L5A · PDBe 4L5A · UniProt I0B503
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