MolNFT v1 · #66197 · protein
1.5 ångström crystal structure of glucose-6-phosphate isomerase from vibrio cholerae.
3HJB: “1.5 ångström crystal structure of glucose-6-phosphate isomerase from vibrio cholerae.”. X-ray diffraction, 3 ligands (CA, NA, CL), 17 pockets (best druggability 0.77). MolNFT v1 #66197 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3HJB
- Type
- protein
- Length
- 2,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase
- EC
- 5.3.1.9
- UniProt
- Q9KUY4
- Ligands
- CA, NA, CL
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 551 | 55% helix, 11% strand | Q9KUY4 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains B, C
- CL · Chloride ion · ion · 26 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.77 | 0.79 | 78 | CA |
| 2 | 1011 | 0.77 | 0.79 | 68 | CA |
| 3 | 599 | 0.75 | 0.82 | 59 | empty |
| 4 | 546 | 0.73 | 0.81 | 52 | empty |
| 5 | 549 | 0.72 | 0.81 | 50 | empty |
Interfaces
4 interfaces between chains.
- A–B · 6101 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 6100 Ų buried · 80 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3HJB · 1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae. · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KUY4 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase (Q9KUY4) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9KUY4
- Elsewhere: RCSB PDB 3HJB · PDBe 3HJB · UniProt Q9KUY4
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