MolNFT v1 · #146437 · protein
Butelase 1: auto-catalytic cleavage as an evolutionary constraint for macrocyclizing endopeptidases
6DHI · Asparaginyl endopeptidase: “Butelase 1: auto-catalytic cleavage as an evolutionary constraint for macrocyclizing endopeptidases”. X-ray diffraction, 1 ligand (SNN), 20 pockets (best druggability 0.71). MolNFT v1 #146437 on…
- PDB
- 6DHI
- Type
- protein
- Length
- 1,679 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparaginyl endopeptidase
- EC
- 3.4.22.34
- UniProt
- A0A060D9Z7
- Ligands
- SNN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparaginyl endopeptidase (EC 3.4.22.34) | protein | 416 | 42% helix, 11% strand | A0A060D9Z7 |
| B | Asparaginyl endopeptidase (EC 3.4.22.34) | protein | 430 | 40% helix, 10% strand | A0A060D9Z7 |
| C | Asparaginyl endopeptidase (EC 3.4.22.34) | protein | 428 | 41% helix, 11% strand | A0A060D9Z7 |
| D | Asparaginyl endopeptidase (EC 3.4.22.34) | protein | 405 | 43% helix, 11% strand | A0A060D9Z7 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.71 | 0.79 | 60 | empty |
| 2 | 192 | 0.67 | 0.86 | 33 | empty |
| 3 | 263 | 0.62 | 0.81 | 36 | empty |
| 4 | 421 | 0.61 | 0.76 | 46 | empty |
| 5 | 281 | 0.61 | 0.79 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1067 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1064 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 541 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 covalent (disulfide, covalent ligand).
Compared structures
- 6DHI · Butelase 1: Auto-Catalytic Cleavage as an Evolutionary Constraint for Macrocyclizing… · the same entry in another collection · 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 A0A060D9Z7
- Elsewhere: RCSB PDB 6DHI · PDBe 6DHI · UniProt A0A060D9Z7
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