Research workbench
Crystal structure of a clostripain (PARMER_00083) from parabacteroides merdae atcc 43184 at 1.70 a resolution
Analyse Crystal structure of a clostripain (PARMER_00083) from parabacteroides merdae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UWS
- Type
- protein
- Length
- 700 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- A7A9N3
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 124 | 29% helix, 37% strand | A7A9N3 |
| B, D | Hypothetical protein | protein | 228 | 42% helix, 21% strand | A7A9N3 |
| C | Hypothetical protein | protein | 120 | 30% helix, 33% strand | A7A9N3 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.78 | 0.80 | 84 | EDO |
| 2 | 190 | 0.51 | 0.77 | 30 | empty |
| 3 | 60 | 0.27 | 0.73 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2672 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2621 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 252 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 177 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 80 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3UWS · Crystal structure of a clostripain (PARMER_00083) from Parabacteroides merdae ATCC 43184… · 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 A7A9N3
- Elsewhere: RCSB PDB 3UWS · PDBe 3UWS · UniProt A7A9N3
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