Research workbench
Active site distortion is sufficient for proteinase inhibit second crystal structure of covalent serpin-proteinase complex
Analyse Active site distortion is sufficient for proteinase inhibit second crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D26
- Type
- protein
- Length
- 589 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1-antitrypsin; Elastase-1
- EC
- 3.4.21.36
- UniProt
- P01009, P00772
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1-antitrypsin | protein | 336 | 23% helix, 28% strand | P01009 |
| B | Alpha-1-antitrypsin | protein | 30 | 0% helix, 37% strand | P01009 |
| C | Elastase-1 (EC 3.4.21.36) | protein | 223 | 8% helix, 33% strand | P00772 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.76 | 0.97 | 26 | empty |
| 2 | 613 | 0.74 | 0.81 | 67 | empty |
| 3 | 305 | 0.71 | 0.85 | 45 | empty |
| 4 | 97 | 0.68 | 0.91 | 26 | empty |
| 5 | 53 | 0.68 | 0.96 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1977 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2D26 · Active site distortion is sufficient for proteinase inhibit second crystal structure of… · 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 C against A, TM-score 0.96
- P01009 · AlphaFold monomer V2.0 prediction for alpha-1-antitrypsin (P01009) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P01009
- Every structure of UniProt P00772
- Elsewhere: RCSB PDB 2D26 · PDBe 2D26 · UniProt P01009 · UniProt P00772
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