MolNFT v1 · #86101 · protein
Crystal structure of active legumain in complex with aan-cmk
4AWB: “Crystal structure of active legumain in complex with aan-cmk”. X-ray diffraction, 6 ligands (PHQ, ZSN, NAG), 3 pockets (best druggability 0.60). MolNFT v1 #86101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AWB
- Type
- protein
- Length
- 527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legumain; Z-ala-ala-azaasn-chloromethylketone
- EC
- 3.4.22.34
- UniProt
- Q99538
- Ligands
- PHQ, ZSN, NAG, HG, 0QE, SO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Legumain (EC 3.4.22.34) | protein | 261 | 32% helix, 21% strand | Q99538 |
| B | Legumain (EC 3.4.22.34) | protein | 262 | 31% helix, 21% strand | Q99538 |
| I, J | Z-ala-ala-azaasn-chloromethylketone | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains A, B, I, J
- ZSN · 1-(2-amino-2-oxoethyl)hydrazinecarboxylic acid · ligand · 2 copies · chains A, B, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- HG · Mercury (II) ion · metal · 4 copies · chains A, B
- 0QE · Chloromethane · ion · 2 copies · chains A, B, I, J
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.60 | 0.78 | 41 | HG |
| 2 | 242 | 0.55 | 0.78 | 33 | HG |
| 3 | 62 | 0.30 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 752 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 184 Ų buried · 2 hydrogen bonds · protein-protein
- B–J · 183 Ų buried · 3 hydrogen bonds · protein-protein
- B–I · 118 Ų buried · 1 hydrogen bond · protein-protein
- A–J · 117 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 covalent (N-glycosylation, covalent ligand).
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 Q99538
- Elsewhere: RCSB PDB 4AWB · PDBe 4AWB · UniProt Q99538
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