Research workbench
Crystal structure of ribose-1,5-bisphosphate isomerase from pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate and AMP
Analyse Crystal structure of ribose-1,5-bisphosphate isomerase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFU
- Type
- protein
- Length
- 966 residues
- Chains
- 3
- 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
- RUB, AMP, K
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribose-1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 322 | 51% helix, 13% strand | O57947 |
Ligands and binding sites
- RUB · Ribulose-1,5-diphosphate · ligand · 3 copies · chains A, B, C
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.77 | 0.80 | 91 | AMP |
| 2 | 87 | 0.68 | 0.93 | 26 | RUB |
| 3 | 91 | 0.67 | 0.92 | 25 | RUB |
| 4 | 87 | 0.66 | 0.92 | 28 | RUB |
| 5 | 228 | 0.59 | 0.80 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 734 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 731 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 719 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YFU · Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in… · 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 5YFU · PDBe 5YFU · UniProt O57947
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