MolNFT v1 · #151057 · protein
The crystal structure of bsap, a zinc aminopeptidase from bacillus subtilis (medium resolution)
6HC7 · Aminopeptidase Y (arg lys leu preference): “The crystal structure of bsap, a zinc aminopeptidase from bacillus subtilis (medium resolution)”. X-ray diffraction, 3 ligands (ZN, CL, SO4), 13 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6HC7
- Type
- protein
- Length
- 1,218 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase Y (arg lys leu preference)
- UniProt
- A0A164UP62
- Ligands
- ZN, CL, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aminopeptidase Y (arg lys leu preference) | protein | 406 | 33% helix, 26% strand | A0A164UP62 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.75 | 0.84 | 60 | empty |
| 2 | 391 | 0.75 | 0.85 | 52 | empty |
| 3 | 453 | 0.73 | 0.83 | 51 | empty |
| 4 | 723 | 0.71 | 0.77 | 76 | SO4, CL |
| 5 | 450 | 0.62 | 0.76 | 50 | SO4, ACT |
Interfaces
3 interfaces between chains.
- A–C · 317 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 226 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HC7 · The crystal structure of BSAP, a zinc aminopeptidase from Bacillus subtilis (medium… · the same entry in another collection · chain B against B, 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 A0A164UP62
- Elsewhere: RCSB PDB 6HC7 · PDBe 6HC7 · UniProt A0A164UP62
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