MolNFT v1 · #82776 · protein
Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from streptcoccus agalactiae
3VXD · Putative uncharacterized protein GBS1889: “Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from streptcoccus agalactiae”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.77). MolNFT v1 #82776 on…
- PDB
- 3VXD
- Type
- protein
- Length
- 1,424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein GBS1889
- EC
- 3.2.1.-
- UniProt
- Q8E372
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein GBS1889 (EC 3.2.1.-) | protein | 358 | 58% helix, 9% strand | Q8E372 |
| B | Putative uncharacterized protein GBS1889 (EC 3.2.1.-) | protein | 354 | 58% helix, 7% strand | Q8E372 |
| C | Putative uncharacterized protein GBS1889 (EC 3.2.1.-) | protein | 359 | 59% helix, 8% strand | Q8E372 |
| D | Putative uncharacterized protein GBS1889 (EC 3.2.1.-) | protein | 353 | 59% helix, 7% strand | Q8E372 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.77 | 0.95 | 31 | empty |
| 2 | 798 | 0.74 | 0.79 | 64 | empty |
| 3 | 511 | 0.62 | 0.75 | 26 | empty |
| 4 | 155 | 0.47 | 0.76 | 21 | empty |
| 5 | 146 | 0.45 | 0.76 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 927 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 926 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3VXD · Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8E372 · AlphaFold monomer V2.0 prediction for unsaturated chondroitin disaccharide hydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8E372
- Elsewhere: RCSB PDB 3VXD · PDBe 3VXD · UniProt Q8E372
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