Research workbench
Thermolysin complexed with Z-D-glutamic acid (benzyloxycarbonyl-D- glutamic acid)
Analyse Thermolysin complexed with Z-D-glutamic acid (benzyloxycarbonyl-D- glutamic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KR6
- 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
- PHQ, DGL, CA, ZN
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermolysin (EC 3.4.24.27) | protein | 316 | 41% helix, 17% strand | P00800 |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A
- DGL · D-glutamic acid · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.51 | 0.80 | 24 | ZN, PHQ, DGL |
Compared structures
- 1KR6 · Thermolysin complexed with Z-D-Glutamic acid (benzyloxycarbonyl-D-Glutamic acid) · the same entry in another collection · chain A against A, TM-score 1.00
- P00800 · AlphaFold monomer V2.0 prediction for thermolysin (P00800) · 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 P00800
- Elsewhere: RCSB PDB 1KR6 · PDBe 1KR6 · UniProt P00800
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