Research workbench
The refined 2.4 ångströms X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction
Analyse The refined 2.4 ångströms X-ray crystal structure of recombinant human stefin B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1STF
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.37
- Source
- Carica papaya; Homo sapiens
- Molecule
- Papain; Stefin B (cystatin B)
- EC
- 3.4.22.2
- UniProt
- P00784, P04080
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · resolution 2.37 · 2 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Papain (EC 3.4.22.2) | protein | 212 | 26% helix, 21% strand | P00784 |
| I | Stefin B (cystatin B) | protein | 98 | 19% helix, 40% strand | P04080 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.27 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- E–I · 917 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1STF · The refined 2.4 ångströms X-ray crystal structure of recombinant human stefin B in… · the same entry in another collection · chain E against E, TM-score 1.00
- P00784 · AlphaFold monomer V2.0 prediction for papain (P00784) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P04080 · AlphaFold monomer V2.0 prediction for cystatin-B (P04080) · a predicted model of the same protein · chain I against A, TM-score 0.97
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 P00784
- Every structure of UniProt P04080
- Elsewhere: RCSB PDB 1STF · PDBe 1STF · UniProt P00784 · UniProt P04080
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