MolNFT v1 · #82422 · protein
Crystal structure of dextranase from streptococcus mutans
3VMN: “Crystal structure of dextranase from streptococcus mutans”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.62). MolNFT v1 #82422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VMN
- Type
- protein
- Length
- 633 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dextranase
- EC
- 3.2.1.11
- UniProt
- F5BA50
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dextranase (EC 3.2.1.11) | protein | 633 | 24% helix, 32% strand | F5BA50 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.62 | 0.78 | 36 | empty |
| 2 | 221 | 0.53 | 0.77 | 28 | empty |
| 3 | 82 | 0.36 | 0.76 | 26 | empty |
| 4 | 52 | 0.32 | 0.78 | 19 | empty |
Compared structures
- 3VMN · Crystal structure of dextranase from Streptococcus mutans · 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 F5BA50
- Elsewhere: RCSB PDB 3VMN · PDBe 3VMN · UniProt F5BA50
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