Research workbench
Porcine pancreatic elastase complexed with beta-casomorphin-7 and lys- ala-NH2 at pH 5.0
Analyse Porcine pancreatic elastase complexed with beta-casomorphin-7 and lys- ala-NH2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BD3
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-casomorphin-7; Elastase-1
- EC
- 3.4.21.36
- UniProt
- P00772
- Ligands
- LYS, ALA, CA, SO4
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Beta-casomorphin-7 | protein | 4 | 0% helix, 50% strand | — |
| A | Elastase-1 (EC 3.4.21.36) | protein | 240 | 11% helix, 40% strand | P00772 |
Ligands and binding sites
- LYS · Lysine · ligand · chains P, A
- ALA · Alanine · ligand · chains A
- 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
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 | 50 | 0.53 | 0.88 | 15 | empty |
Interfaces
1 interface between chains.
- P–A · 402 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2BD3 · Porcine pancreatic elastase complexed with beta-casomorphin-7 and Lys-Ala-NH2 at pH 5.0 · the same entry in another collection · chain P against P, 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 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 P00772
- Elsewhere: RCSB PDB 2BD3 · PDBe 2BD3 · UniProt P00772
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