MolNFT v1 · #127439 · protein
Glycoside hydrolase BT_0986
5MWK · Glycoside hydrolase family 2, sugar binding protein: “Glycoside hydrolase BT_0986”. X-ray diffraction, 8 ligands (8OQ, 8PK, RAM), 14 pockets (best druggability 0.81). MolNFT v1 #127439 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MWK
- Type
- protein
- Length
- 1,040 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 2, sugar binding protein
- UniProt
- Q8A931
- Ligands
- 8OQ, 8PK, RAM, GAL, ARA, CA, BR, IOD
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 2, sugar binding protein | protein | 1040 | 24% helix, 32% strand | Q8A931 |
Ligands and binding sites
- 8OQ · alpha-D-aceric acid · ligand
- 8PK · 4-O-[(1R)-1-hydroxyethyl]-2-O-methyl-alpha-L-fucopyranose · ligand · chains A
- RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- ARA · alpha-L-arabinopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- BR · Bromide ion · ion · 2 copies · chains A
- IOD · Iodide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.81 | 0.85 | 117 | empty |
| 2 | 105 | 0.66 | 0.90 | 21 | empty |
| 3 | 255 | 0.62 | 0.81 | 35 | GAL, ARA, RAM, 8PK, CA |
| 4 | 54 | 0.59 | 0.91 | 22 | BR |
| 5 | 334 | 0.58 | 0.77 | 36 | empty |
Compared structures
- 5MWK · Glycoside hydrolase BT_0986 · 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 Q8A931
- Elsewhere: RCSB PDB 5MWK · PDBe 5MWK · UniProt Q8A931
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