MolNFT v1 · #126152 · protein
Crystal structure of yvad-cmk bound human legumain (aep) in complex with compound 11B
5LU8 · Ac-tyr-val-ala-asp-chloromethylketone: “Crystal structure of yvad-cmk bound human legumain (aep) in complex with compound 11B”. X-ray diffraction, 7 ligands (ACE, SNN, EMC), 1 pocket (best druggability 0.32). MolNFT v1 #126152 on…
- PDB
- 5LU8
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ac-tyr-val-ala-asp-chloromethylketone; Legumain
- EC
- 3.4.22.34
- UniProt
- Q99538
- Ligands
- ACE, SNN, EMC, 5KN, NAG, SO4, 0QE
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ac-tyr-val-ala-asp-chloromethylketone | protein | 4 | 0% helix, 25% strand | — |
| A | Legumain (EC 3.4.22.34) | protein | 262 | 33% helix, 20% strand | Q99538 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains C, A
- SNN · L-3-aminosuccinimide · ligand · chains C, A
- EMC · Ethyl mercury ion · ligand · chains A
- 5KN · 2,4-di(morpholin-4-yl)aniline · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- 0QE · Chloromethane · ion · chains C, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- C–A · 382 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 glycan (covalent ligand, N-glycosylation).
Compared structures
- 5LU8 · Crystal structure of yvad-cmk bound human legumain (aep) in complex with compound 11B · the same entry in another collection · chain C against C, TM-score 1.00
- Q99538 · AlphaFold monomer V2.0 prediction for legumain (Q99538) · a predicted model of the same protein · chain A 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 Q99538
- Elsewhere: RCSB PDB 5LU8 · PDBe 5LU8 · UniProt Q99538
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