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Endothiapepsin-DB5 complex.
Analyse Endothiapepsin-DB5 complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3URI
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothiapepsin; DB5 peptide
- EC
- 3.4.23.22
- UniProt
- P11838
- Ligands
- SUI, 13E
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothiapepsin (EC 3.4.23.22) | protein | 328 | 12% helix, 47% strand | P11838 |
| B | DB5 peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- SUI · (3-amino-2,5-dioxo-1-pyrrolidinyl)acetic acid · ligand · chains A
- 13E · N-[(2S)-2-amino-3-phenylpropyl]-L-methionine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.62 | 0.85 | 31 | 13E |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
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 P11838
- Elsewhere: RCSB PDB 3URI · PDBe 3URI · UniProt P11838
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