Research workbench
Tetragonal thermolysin cryocooled to 100 K with 25% XYLOSE/25% mpd as cryoprotectant
Analyse Tetragonal thermolysin cryocooled to 100 K with 25% XYLOSE/25% mpd as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UUB
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermolysin
- EC
- 3.4.24.27
- UniProt
- P00800
- Ligands
- XYP, ZN, CA, CL
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermolysin (EC 3.4.24.27) | protein | 316 | 43% helix, 18% strand | P00800 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A
- ZN · Zinc ion · metal · 7 copies · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · 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 | 95 | 0.40 | 0.77 | 19 | ZN, MRD |
Compared structures
- 5UUB · Tetragonal thermolysin cryocooled to 100 K with 25% xylose/25% mpd as cryoprotectant · 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 P00800
- Elsewhere: RCSB PDB 5UUB · PDBe 5UUB · UniProt P00800
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