Research workbench
Crystal structure of ribose-5-phosphate isomerase a from bartonella henselae
Analyse Crystal structure of ribose-5-phosphate isomerase a from bartonella henselae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HHE
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase a
- EC
- 5.3.1.6
- UniProt
- Q6G3V6
- Ligands
- 5RP, K, CL
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 233 | 34% helix, 26% strand | Q6G3V6 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.45 | 0.79 | 34 | 5RP |
| 2 | 149 | 0.44 | 0.75 | 32 | empty |
| 3 | 121 | 0.44 | 0.77 | 28 | empty |
| 4 | 98 | 0.39 | 0.77 | 24 | 5RP |
| 5 | 61 | 0.30 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1200 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3HHE · Crystal structure of ribose-5-phosphate isomerase A from Bartonella henselae · the same entry in another collection · chain A against A, TM-score 1.00
- Q6G3V6 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (Q6G3V6) · 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 Q6G3V6
- Elsewhere: RCSB PDB 3HHE · PDBe 3HHE · UniProt Q6G3V6
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