Research workbench
Crystal structure of glucosamine-6-phosphate deaminase from vibrio cholerae
Analyse Crystal structure of glucosamine-6-phosphate deaminase from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R7T
- Type
- protein
- Length
- 795 residues
- Chains
- 3
- 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
- MG, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 | 265 | 40% helix, 15% strand | Q9KKS5 |
| C | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 264 | 44% helix, 16% strand | Q9KKS5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A, C
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.72 | 0.76 | 74 | CL |
| 2 | 781 | 0.70 | 0.76 | 69 | GOL |
| 3 | 554 | 0.66 | 0.77 | 53 | FMT |
| 4 | 209 | 0.47 | 0.75 | 27 | empty |
| 5 | 183 | 0.43 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 561 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4R7T · Crystal structure of glucosamine-6-phosphate deaminase from Vibrio cholerae · 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 B 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 Q9KKS5
- Elsewhere: RCSB PDB 4R7T · PDBe 4R7T · UniProt Q9KKS5
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