MolNFT v1 · #140596 · protein
Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from pyrococcus horikoshii OT3 in complex with ribose-1,5- bisphosphate and AMP
5YFX · Ribose 1,5-bisphosphate isomerase: “Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from pyrococcus horikoshii OT3 in complex…”. X-ray diffraction, 2 ligands (RI2, AMP), 3 pockets (best druggability 0.69). MolNFT…
- PDB
- 5YFX
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose 1,5-bisphosphate isomerase
- EC
- 5.3.1.29
- UniProt
- O57947
- Ligands
- RI2, AMP
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 321 | 51% helix, 13% strand | O57947 |
Ligands and binding sites
- RI2 · 1,5-di-O-phosphono-alpha-D-ribofuranose · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.69 | 0.93 | 32 | RI2 |
| 2 | 222 | 0.57 | 0.79 | 39 | empty |
| 3 | 55 | 0.26 | 0.73 | 15 | empty |
Compared structures
- 5YFX · Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O57947 · AlphaFold monomer V2.0 prediction for ribose 1,5-bisphosphate isomerase (O57947) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O57947
- Elsewhere: RCSB PDB 5YFX · PDBe 5YFX · UniProt O57947
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