MolNFT v1 · #75531 · protein
Structure of DUF89 from saccharomyces cerevisiae co-crystallized with F6P.
3PT1 · UPF0364 protein YMR027W: “Structure of DUF89 from saccharomyces cerevisiae co-crystallized with F6P.”. X-ray diffraction, 2 ligands (F6P, MG), 2 pockets (best druggability 0.66). MolNFT v1 #75531 on GenesisL1: 3D structure, binding…
- PDB
- 3PT1
- Type
- protein
- Length
- 464 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0364 protein YMR027W
- UniProt
- Q04371
- Ligands
- F6P, MG
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0364 protein YMR027W | protein | 464 | 56% helix, 10% strand | Q04371 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.66 | 0.80 | 45 | F6P, MG |
| 2 | 124 | 0.40 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3PT1 · Structure of DUF89 from Saccharomyces cerevisiae co-crystallized with F6P. · the same entry in another collection · chain A against A, TM-score 1.00
- Q04371 · AlphaFold monomer V2.0 prediction for damage-control phosphatase YMR027W (Q04371) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q04371
- Elsewhere: RCSB PDB 3PT1 · PDBe 3PT1 · UniProt Q04371
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