MolNFT v1 · #58821 · protein
Crystal structure of escherichia COLI signal peptide peptidase (sppa), native crystals
3BF0 · Protease 4: “Crystal structure of escherichia COLI signal peptide peptidase (sppa), native crystals”. X-ray diffraction, 16 pockets (best druggability 0.78). MolNFT v1 #58821 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3BF0
- Type
- protein
- Length
- 1,902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease 4
- EC
- 3.4.21.-
- UniProt
- P08395
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease 4 (EC 3.4.21.-) | protein | 474 | 42% helix, 25% strand | P08395 |
| B | Protease 4 (EC 3.4.21.-) | protein | 474 | 41% helix, 24% strand | P08395 |
| C | Protease 4 (EC 3.4.21.-) | protein | 478 | 42% helix, 24% strand | P08395 |
| D | Protease 4 (EC 3.4.21.-) | protein | 476 | 42% helix, 24% strand | P08395 |
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.78 | 0.80 | 109 | empty |
| 2 | 888 | 0.77 | 0.80 | 87 | empty |
| 3 | 999 | 0.77 | 0.79 | 89 | empty |
| 4 | 730 | 0.71 | 0.78 | 76 | empty |
| 5 | 520 | 0.70 | 0.79 | 46 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1587 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1542 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1510 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1457 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3BF0 · Crystal structure of Escherichia coli Signal peptide peptidase (SppA), Native crystals · the same entry in another collection · chain D against D, TM-score 1.00
- P08395 · AlphaFold monomer V2.0 prediction for protease 4 (P08395) · a predicted model of the same protein · chain B 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 P08395
- Elsewhere: RCSB PDB 3BF0 · PDBe 3BF0 · UniProt P08395
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