MolNFT v1 · #25015 · protein
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from bacillus sp. GL1 at 1.8 a resolution
1VD5: “Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan…”. X-ray diffraction, 1 ligand (GLY), 1 pocket (best druggability 0.45). MolNFT v1 #25015 on GenesisL1: 3D structure…
- PDB
- 1VD5
- Type
- protein
- Length
- 377 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unsaturated glucuronyl hydrolase
- EC
- 3.2.1.-
- UniProt
- Q9RC92
- Ligands
- GLY
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unsaturated glucuronyl hydrolase (EC 3.2.1.-) | protein | 377 | 54% helix, 10% strand | Q9RC92 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.45 | 0.78 | 21 | GLY, DTT |
Compared structures
- 1VD5 · Crystal Structure of Unsaturated Glucuronyl Hydrolase, Responsible for the Degradation of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RC92 · AlphaFold monomer V2.0 prediction for unsaturated glucuronyl hydrolase (Q9RC92) · a predicted model of the same protein · 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 Q9RC92
- Elsewhere: RCSB PDB 1VD5 · PDBe 1VD5 · UniProt Q9RC92
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