MolNFT v1 · #151056 · protein
The structure of bsap, a zinc aminopeptidase from bacillus subtilis
6HC6 · Aminopeptidase ywad: “The structure of bsap, a zinc aminopeptidase from bacillus subtilis”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.74). MolNFT v1 #151056 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HC6
- Type
- protein
- Length
- 1,222 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase ywad
- EC
- 3.4.11.6, 3.4.11.10
- UniProt
- P25152
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminopeptidase ywad (EC 3.4.11.6, 3.4.11.10) | protein | 407 | 33% helix, 25% strand | P25152 |
| C | Aminopeptidase ywad (EC 3.4.11.6, 3.4.11.10) | protein | 408 | 33% helix, 25% strand | P25152 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- ACT · Acetate ion · additive · 10 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.74 | 0.86 | 50 | empty |
| 2 | 341 | 0.74 | 0.86 | 55 | empty |
| 3 | 255 | 0.73 | 0.87 | 36 | empty |
| 4 | 512 | 0.65 | 0.77 | 50 | ACT |
| 5 | 484 | 0.63 | 0.76 | 50 | ACT |
Interfaces
3 interfaces between chains.
- A–C · 399 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 312 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
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 P25152
- Elsewhere: RCSB PDB 6HC6 · PDBe 6HC6 · UniProt P25152
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