Research workbench
Structure of a protease 1
Analyse Structure of a protease 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KQX
- Type
- protein
- Length
- 6,145 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M17 leucyl aminopeptidase
- EC
- 3.4.11.1
- UniProt
- Q8IL11
- Ligands
- ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 514 | 36% helix, 22% strand | Q8IL11 |
| B, H | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 510 | 36% helix, 22% strand | Q8IL11 |
| C | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 518 | 36% helix, 22% strand | Q8IL11 |
| D, J | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 514 | 35% helix, 22% strand | Q8IL11 |
| E, K | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 509 | 35% helix, 22% strand | Q8IL11 |
| F | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 510 | 35% helix, 22% strand | Q8IL11 |
| I | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 515 | 36% helix, 22% strand | Q8IL11 |
| L | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 508 | 35% helix, 22% strand | Q8IL11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 16 copies · chains A, D, B, C, E, F, G, I, H, J, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 54 copies · chains A, B, C, D, E, F, G, L, H, I, J, K
- 2PE · Nonaethylene glycol · additive · 4 copies · chains B, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.78 | 0.82 | 76 | empty |
| 2 | 842 | 0.74 | 0.78 | 69 | CO3, 1PE |
| 3 | 884 | 0.74 | 0.78 | 72 | CO3, 1PE |
| 4 | 828 | 0.74 | 0.78 | 79 | 1PE |
| 5 | 836 | 0.73 | 0.78 | 72 | CO3, 1PE |
Interfaces
26 interfaces between chains.
- H–I · 1501 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1497 Ų buried · 25 hydrogen bonds · protein-protein
- G–I · 1488 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1480 Ų buried · 24 hydrogen bonds · protein-protein
- J–K · 1446 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3KQX · Structure of a protease 1 · 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 Q8IL11
- Elsewhere: RCSB PDB 3KQX · PDBe 3KQX · UniProt Q8IL11
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