MolNFT v1 · #93215 · protein
Lyngbyastatin 7-porcine pancreatic elastase co-crystal structure
4GVU · Chymotrypsin-like elastase family member 1: “Lyngbyastatin 7-porcine pancreatic elastase co-crystal structure”. X-ray diffraction, 3 ligands (6NA, CA, SO4), 2 pockets (best druggability 0.57). MolNFT v1 #93215 on GenesisL1: 3D…
- PDB
- 4GVU
- Type
- protein
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chymotrypsin-like elastase family member 1; Lyngbyastatin 7
- EC
- 3.4.21.36
- UniProt
- P00772
- Ligands
- 6NA, CA, SO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chymotrypsin-like elastase family member 1 (EC 3.4.21.36) | protein | 240 | 11% helix, 38% strand | P00772 |
| B | Lyngbyastatin 7 | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- 6NA · Hexanoic acid · ligand · chains A, B
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.57 | 0.90 | 20 | empty |
| 2 | 52 | 0.30 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 459 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified, 1 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 4GVU · Lyngbyastatin 7-Porcine Pancreatic Elastase Co-crystal Structure · the same entry in another collection · chain A against A, TM-score 1.00
- P00772 · AlphaFold monomer V2.0 prediction for chymotrypsin-like elastase family member 1 (P00772) · a predicted model of the same protein · chain A 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 P00772
- Elsewhere: RCSB PDB 4GVU · PDBe 4GVU · UniProt P00772
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