Research workbench
Binding structure of elastase inhibitor scyptolin a
Analyse Binding structure of elastase inhibitor scyptolin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OKX
- Type
- protein
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elastase 1; Scyptolin a
- EC
- 3.4.21.36
- UniProt
- P00772
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Elastase 1 (EC 3.4.21.36) | protein | 240 | 11% helix, 38% strand | P00772 |
| C, D | Scyptolin a | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- 1BO · 1-butanol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.71 | 0.88 | 28 | empty |
| 2 | 67 | 0.58 | 0.89 | 18 | empty |
| 3 | 63 | 0.56 | 0.89 | 18 | empty |
| 4 | 172 | 0.45 | 0.75 | 26 | empty |
| 5 | 122 | 0.38 | 0.74 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 649 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 598 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 595 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 208 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 196 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified, 2 covalent (disulfide, nonstandard, additive adduct).
Compared structures
- 1OKX · Binding Structure of Elastase Inhibitor Scyptolin A · 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 1OKX · PDBe 1OKX · UniProt P00772
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