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Crystal structure of glucosamine 6-phosphate deaminase (nagb) with GLCN6P from S. mutans
Analyse Crystal structure of glucosamine 6-phosphate deaminase (nagb) with GLCN6P from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RI1
- Type
- protein
- Length
- 470 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
- Q8DV70
- Ligands
- GLP
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 235 | 36% helix, 20% strand | Q8DV70 |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.70 | 0.77 | 55 | GLP |
| 2 | 412 | 0.64 | 0.78 | 34 | empty |
| 3 | 295 | 0.60 | 0.78 | 41 | GLP |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2RI1 · Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DV70 · AlphaFold monomer V2.0 prediction for glucosamine-6-phosphate deaminase (Q8DV70) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q8DV70
- Elsewhere: RCSB PDB 2RI1 · PDBe 2RI1 · UniProt Q8DV70
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