MolNFT v1 · #132539 · protein
Pandda analysis group deposition -- endothiapepsin in complex with fragment F2X-entry G08, dmso-free
5R28: “Pandda analysis group deposition -- endothiapepsin in complex with fragment F2X-entry G08, dmso-free”. X-ray diffraction, 1 ligand (RDJ), 1 pocket (best druggability 0.58). MolNFT v1 #132539 on GenesisL1: 3D structure, binding sites…
- PDB
- 5R28
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothiapepsin
- EC
- 3.4.23.22
- UniProt
- P11838
- Ligands
- RDJ
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothiapepsin (EC 3.4.23.22) | protein | 330 | 11% helix, 45% strand | P11838 |
Ligands and binding sites
- RDJ · N-ethyl-2-{[5-(propan-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetamide · ligand · chains A
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 | 328 | 0.58 | 0.76 | 38 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5R28 · PanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry… · the same entry in another collection · chain A against A, TM-score 1.00
- P11838 · AlphaFold monomer V2.0 prediction for endothiapepsin (P11838) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 5R28 · PDBe 5R28 · UniProt P11838
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