MolNFT v1 · #32257 · protein
Structure and kinetics of a monomeric glucosamine-6- phosphate deaminase: missing link of the nagb superfamily
2BKV · Glucosamine-6-phosphate deaminase: “Structure and kinetics of a monomeric glucosamine-6- phosphate deaminase: missing link of the nagb superfamily”. X-ray diffraction, 1 ligand (PGA), 2 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 2BKV
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine-6-phosphate deaminase
- EC
- 3.5.99.6
- UniProt
- O35000
- Ligands
- PGA
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 241 | 41% helix, 18% strand | O35000 |
| B | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 242 | 42% helix, 18% strand | O35000 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.77 | 0.84 | 67 | PGA |
| 2 | 245 | 0.72 | 0.87 | 41 | PGA |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2BKV · Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of… · the same entry in another collection · chain A against A, TM-score 1.00
- O35000 · AlphaFold monomer V2.0 prediction for glucosamine-6-phosphate deaminase 1 (O35000) · a predicted model of the same protein · chain B 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 O35000
- Elsewhere: RCSB PDB 2BKV · PDBe 2BKV · UniProt O35000
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