MolNFT v1 · #120410 · protein
Endo-beta-1,2-glucanase from chitinophaga pinensis - sophorotriose and glucose complex
5GZK · Uncharacterized protein: “Endo-beta-1,2-glucanase from chitinophaga pinensis - sophorotriose and glucose complex”. X-ray diffraction, 4 ligands (BGC, K, PO4), 9 pockets (best druggability 0.76). MolNFT v1 #120410 on GenesisL1: 3D…
- PDB
- 5GZK
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- C7PIC2
- Ligands
- BGC, K, PO4, CL
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 418 | 45% helix, 13% strand | C7PIC2 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PG4 · Tetraethylene glycol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.76 | 0.87 | 31 | PG4, 1PE |
| 2 | 54 | 0.57 | 0.90 | 13 | empty |
| 3 | 56 | 0.57 | 0.90 | 14 | empty |
| 4 | 266 | 0.54 | 0.75 | 40 | BGC |
| 5 | 218 | 0.52 | 0.76 | 39 | BGC |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GZK · Endo-beta-1,2-glucanase from Chitinophaga pinensis - sophorotriose and glucose complex · 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 C7PIC2
- Elsewhere: RCSB PDB 5GZK · PDBe 5GZK · UniProt C7PIC2
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