MolNFT v1 · #58820 · protein
Crystal structure of escherichia COLI signal peptide peptidase (sppa), semet crystals
3BEZ · Protease 4: “Crystal structure of escherichia COLI signal peptide peptidase (sppa), semet crystals”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #58820 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3BEZ
- Type
- protein
- Length
- 1,901 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
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease 4 (EC 3.4.21.-) | protein | 473 | 42% helix, 23% strand | P08395 |
| C | Protease 4 (EC 3.4.21.-) | protein | 476 | 42% helix, 24% strand | P08395 |
| D | Protease 4 (EC 3.4.21.-) | protein | 479 | 41% helix, 23% strand | P08395 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.76 | 0.78 | 108 | empty |
| 2 | 770 | 0.75 | 0.80 | 74 | empty |
| 3 | 1177 | 0.75 | 0.78 | 112 | empty |
| 4 | 721 | 0.72 | 0.78 | 76 | empty |
| 5 | 469 | 0.67 | 0.79 | 50 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1605 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1596 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1571 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1556 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3BEZ · Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals · the same entry in another collection · chain A against A, TM-score 1.00
- P08395 · AlphaFold monomer V2.0 prediction for protease 4 (P08395) · a predicted model of the same protein · chain C 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 3BEZ · PDBe 3BEZ · UniProt P08395
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