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Crystal structure of a hepatocyte growth factor activator inhibitor-1 (hai-1) fragment covering the pkd-like 'internal' domain and kunitz domain 1
Analyse Crystal structure of a hepatocyte growth factor activator inhibitor-1 (hai-1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EZD
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kunitz-type protease inhibitor 1
- UniProt
- O43278
- Ligands
- K
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kunitz-type protease inhibitor 1 | protein | 120 | 14% helix, 40% strand | O43278 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.63 | 0.75 | 45 | empty |
| 2 | 84 | 0.35 | 0.74 | 18 | empty |
| 3 | 83 | 0.31 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1034 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5EZD · Crystal structure of a Hepatocyte growth factor activator inhibitor-1 (HAI-1) fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- O43278 · AlphaFold monomer V2.0 prediction for kunitz-type protease inhibitor 1 (O43278) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 O43278
- Elsewhere: RCSB PDB 5EZD · PDBe 5EZD · UniProt O43278
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