Research workbench
Structure of C. glutamicum glnk
Analyse Structure of C. glutamicum glnk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YC6
- Type
- protein
- Length
- 325 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pii protein
- UniProt
- H7C694
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pii protein | protein | 110 | 29% helix, 44% strand | H7C694 |
| B | Pii protein | protein | 108 | 30% helix, 40% strand | H7C694 |
| C | Pii protein | protein | 107 | 30% helix, 40% strand | H7C694 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.68 | 0.92 | 24 | empty |
| 2 | 300 | 0.65 | 0.81 | 36 | PO4, EDO |
| 3 | 239 | 0.64 | 0.82 | 31 | PO4, EDO |
| 4 | 210 | 0.59 | 0.81 | 30 | PO4, EDO |
Interfaces
3 interfaces between chains.
- B–C · 1354 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1260 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1232 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6YC6 · Structure of C. glutamicum GlnK · the same entry in another collection · 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 H7C694
- Elsewhere: RCSB PDB 6YC6 · PDBe 6YC6 · UniProt H7C694
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