Research workbench
E. COLI aminopeptidase a (pepa)
Analyse E. COLI aminopeptidase a (pepa) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GYT
- Type
- protein
- Length
- 6,036 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosol aminopeptidase
- EC
- 3.4.11.1
- UniProt
- P11648
- Ligands
- ZN, CO3, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Cytosol aminopeptidase (EC 3.4.11.1) | protein | 503 | 40% helix, 20% strand | P11648 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 907 | 0.73 | 0.77 | 80 | empty |
| 2 | 811 | 0.71 | 0.77 | 70 | empty |
| 3 | 771 | 0.71 | 0.77 | 66 | empty |
| 4 | 735 | 0.70 | 0.77 | 62 | empty |
| 5 | 735 | 0.70 | 0.77 | 63 | empty |
Interfaces
27 interfaces between chains.
- K–L · 1222 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1213 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1208 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1204 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1203 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1GYT · E. coli Aminopeptidase A (PepA) · 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 P11648
- Elsewhere: RCSB PDB 1GYT · PDBe 1GYT · UniProt P11648
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.