MolNFT v1 · #118602 · protein
Crystal structure of mutant S12T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase in apo form
5F73: “Crystal structure of mutant S12T of ADENOSINE/METHYLTHIOADENOSINE phosphorylase in apo form”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.86). MolNFT v1 #118602 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F73
- Type
- protein
- Length
- 1,692 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 · 6 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 288 | 32% helix, 25% strand | I0B503 |
| B | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 30% helix, 25% strand | I0B503 |
| C | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 281 | 30% helix, 25% strand | I0B503 |
| D | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 279 | 32% helix, 25% strand | I0B503 |
| E | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 32% helix, 24% strand | I0B503 |
| F | Methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 272 | 32% 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.86 | 0.93 | 66 | empty |
| 2 | 422 | 0.85 | 0.93 | 60 | empty |
| 3 | 500 | 0.74 | 0.82 | 53 | SO4 |
| 4 | 532 | 0.72 | 0.81 | 54 | SO4 |
| 5 | 444 | 0.71 | 0.82 | 50 | SO4 |
Interfaces
7 interfaces between chains.
- D–F · 1218 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1192 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1186 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5F73 · Crystal structure of Mutant S12T of Adenosine/Methylthioadenosine Phosphorylase in APO… · 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 5F73 · PDBe 5F73 · UniProt I0B503
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