MolNFT v1 · #163736 · protein
The crystal structure of pfa-M1 in complex with 7-amino-1,4-dibromo-5, 7,8,9-tetrahydrobenzocyclohepten-6-one
6SBR · M1-family alanyl aminopeptidase: “The crystal structure of pfa-M1 in complex with 7-amino-1,4-dibromo-5, 7,8,9-tetrahydrobenzocyclohepten-6-one”. X-ray diffraction, 3 ligands (L5E, ZN, CL), 11 pockets (best druggability 0.82).…
- PDB
- 6SBR
- 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
- L5E, ZN, CL
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1-family alanyl aminopeptidase (EC 3.4.11.2) | protein | 891 | 45% helix, 21% strand | Q8IEK1 |
Ligands and binding sites
- L5E · [(7~{S})-1,4-bis(bromanyl)-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.82 | 0.85 | 98 | ZN, L5E, GOL |
| 2 | 535 | 0.76 | 0.83 | 52 | empty |
| 3 | 713 | 0.70 | 0.77 | 67 | empty |
| 4 | 76 | 0.65 | 0.92 | 22 | empty |
| 5 | 181 | 0.43 | 0.73 | 27 | empty |
Compared structures
- 6SBR · 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 6SBR · PDBe 6SBR · UniProt Q8IEK1
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