MolNFT v1 · #121033 · protein
Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from vibrio cholerae with beta-D-glucose-6-phosphate and fructose-6-phosphate
5HJ5: “Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from vibrio cholerae with…”. X-ray diffraction, 2 ligands (F6R, BG6), 9 pockets (best druggability 0.75). MolNFT v1 #121033 on GenesisL1: 3D structure…
- PDB
- 5HJ5
- Type
- protein
- Length
- 1,065 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine-6-phosphate deaminase
- EC
- 3.5.99.6
- UniProt
- Q9KKS5
- Ligands
- F6R, BG6
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 266 | 42% helix, 15% strand | Q9KKS5 |
| B | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 267 | 43% helix, 15% strand | Q9KKS5 |
Ligands and binding sites
- F6R · Fructose -6-phosphate · ligand · 4 copies · chains A, B, C, D
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.75 | 0.92 | 31 | F6R |
| 2 | 161 | 0.74 | 0.91 | 33 | F6R |
| 3 | 150 | 0.72 | 0.91 | 27 | F6R |
| 4 | 179 | 0.71 | 0.89 | 34 | F6R |
| 5 | 323 | 0.53 | 0.74 | 39 | empty |
Interfaces
3 interfaces between chains.
- C–D · 256 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 170 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HJ5 · Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KKS5 · AlphaFold monomer V2.0 prediction for glucosamine-6-phosphate deaminase (Q9KKS5) · 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 Q9KKS5
- Elsewhere: RCSB PDB 5HJ5 · PDBe 5HJ5 · UniProt Q9KKS5
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