Research workbench
Complex of clpv N-domain with vipb peptide
Analyse Complex of clpv N-domain with vipb peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZRJ
- Type
- protein
- Length
- 349 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clpb protein; Vipb
- UniProt
- A1EKV2, Q9KN57
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clpb protein | protein | 160 | 58% helix, 4% strand | A1EKV2 |
| B | Clpb protein | protein | 165 | 56% helix, 2% strand | A1EKV2 |
| X | Vipb | protein | 14 | 71% helix, 0% strand | Q9KN57 |
| Y | Vipb | protein | 10 | 80% helix, 0% strand | Q9KN57 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.59 | 0.79 | 32 | empty |
| 2 | 85 | 0.41 | 0.78 | 19 | empty |
| 3 | 91 | 0.39 | 0.77 | 18 | empty |
| 4 | 100 | 0.36 | 0.74 | 15 | empty |
| 5 | 62 | 0.32 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1260 Ų buried · 20 hydrogen bonds · protein-protein
- B–Y · 566 Ų buried · 3 hydrogen bonds · protein-protein
- A–X · 511 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ZRJ · Complex of ClpV N-domain with VipB peptide · 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 A1EKV2
- Every structure of UniProt Q9KN57
- Elsewhere: RCSB PDB 3ZRJ · PDBe 3ZRJ · UniProt A1EKV2 · UniProt Q9KN57
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