MolNFT v1 · #84621 · protein
Structure of a paenibacillus polymyxa xyloglucanase from glycoside hydrolase family 44
3ZQ9: “Structure of a paenibacillus polymyxa xyloglucanase from glycoside hydrolase family 44”. X-ray diffraction, 5 ligands (NOY, BGC, CA), 3 pockets (best druggability 0.60). MolNFT v1 #84621 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ZQ9
- Type
- protein
- Length
- 512 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucanase
- EC
- 3.2.1.4, 3.2.1.151
- UniProt
- Q1A2D0
- Ligands
- NOY, BGC, CA, SO4, CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xyloglucanase (EC 3.2.1.4, 3.2.1.151) | protein | 512 | 31% helix, 26% strand | Q1A2D0 |
Ligands and binding sites
- NOY · (2R,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.60 | 0.78 | 46 | NOY, BGC, EDO |
| 2 | 164 | 0.50 | 0.78 | 22 | empty |
| 3 | 65 | 0.33 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZQ9 · Structure of a Paenibacillus Polymyxa Xyloglucanase from Glycoside Hydrolase Family 44 · 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 Q1A2D0
- Elsewhere: RCSB PDB 3ZQ9 · PDBe 3ZQ9 · UniProt Q1A2D0
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