Research workbench
Crystal structure of ribose-1,5-bisphosphate isomerase from thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5- bisphosphate
Analyse Crystal structure of ribose-1,5-bisphosphate isomerase from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VM6
- Type
- protein
- Length
- 963 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor eif-2B, delta subunit
- EC
- 5.3.1.-
- UniProt
- Q5JFM9
- Ligands
- RI2, MG, CL
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 321 | 51% helix, 13% strand | Q5JFM9 |
Ligands and binding sites
- RI2 · 1,5-di-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, C, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.70 | 0.93 | 34 | RI2 |
| 2 | 74 | 0.68 | 0.94 | 27 | RI2 |
| 3 | 428 | 0.66 | 0.79 | 55 | PEG |
| 4 | 82 | 0.64 | 0.91 | 25 | RI2 |
| 5 | 223 | 0.61 | 0.81 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 742 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 736 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 731 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3VM6 · Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JFM9 · AlphaFold monomer V2.0 prediction for ribose 1,5-bisphosphate isomerase (Q5JFM9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5JFM9
- Elsewhere: RCSB PDB 3VM6 · PDBe 3VM6 · UniProt Q5JFM9
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