Research workbench
Crystal structure of recombinant barley cysteine endoprotease B isoform 2 (ep-B2) in complex with leupeptin
Analyse Crystal structure of recombinant barley cysteine endoprotease B isoform 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FO5
- Type
- protein
- Length
- 908 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine proteinase ep-B 2; ACE-leu-leu-argininal (leupeptin)
- EC
- 3.4.22.-
- UniProt
- P25250
- Ligands
- ACE, SO4
- Pockets
- 9 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cysteine proteinase ep-B 2 (EC 3.4.22.-) | protein | 224 | 28% helix, 21% strand | P25250 |
| E, F, G, H | ACE-leu-leu-argininal (leupeptin) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.50 | 0.75 | 32 | empty |
| 2 | 131 | 0.42 | 0.76 | 32 | empty |
| 3 | 102 | 0.40 | 0.76 | 15 | SO4 |
| 4 | 58 | 0.35 | 0.78 | 14 | empty |
| 5 | 77 | 0.33 | 0.75 | 22 | empty |
Interfaces
8 interfaces between chains.
- C–D · 663 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 414 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 378 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 375 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 2FO5 · Crystal structure of recombinant barley cysteine endoprotease B isoform 2 (EP-B2) in… · the same entry in another collection · chain H against H, TM-score 1.00
- P25250 · AlphaFold monomer V2.0 prediction for cysteine proteinase ep-B 2 (P25250) · a predicted model of the same protein · chain C 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 P25250
- Elsewhere: RCSB PDB 2FO5 · PDBe 2FO5 · UniProt P25250
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