Research workbench
The crystal structure of pfa-M1 in complex with 7-amino-4-phenyl-5,7, 8,9-tetrahydrobenzocyclohepten-6-one
Analyse The crystal structure of pfa-M1 in complex with 7-amino-4-phenyl-5,7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SBQ
- Type
- protein
- Length
- 891 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1-family alanyl aminopeptidase
- EC
- 3.4.11.2
- UniProt
- Q8IEK1
- Ligands
- 7ML, NA, ZN
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1-family alanyl aminopeptidase (EC 3.4.11.2) | protein | 891 | 45% helix, 22% strand | Q8IEK1 |
Ligands and binding sites
- 7ML · [(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- MLI · Malonate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.78 | 0.87 | 55 | 7ML |
| 2 | 290 | 0.72 | 0.85 | 36 | PEG |
| 3 | 696 | 0.70 | 0.77 | 65 | empty |
| 4 | 70 | 0.66 | 0.93 | 20 | empty |
| 5 | 93 | 0.59 | 0.87 | 22 | empty |
Compared structures
- 6SBQ · The crystal structure of PfA-M1 in complex with… · 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 Q8IEK1
- Elsewhere: RCSB PDB 6SBQ · PDBe 6SBQ · UniProt Q8IEK1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.