Research workbench
Negative-stain electron microscopy of E. COLI clpb (bap form bound to clpp)
Analyse Negative-stain electron microscopy of E. COLI clpb (bap form bound to clpp) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D2U
- Type
- protein
- Length
- 4,734 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb
- UniProt
- P63284
- Pockets
- 20 · best druggability 0.58
Structure
electron microscopy · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Chaperone protein clpb | protein | 789 | 0% helix, 0% strand | P63284 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.58 | 0.73 | 76 | empty |
| 2 | 458 | 0.57 | 0.73 | 74 | empty |
| 3 | 441 | 0.56 | 0.73 | 62 | empty |
| 4 | 425 | 0.55 | 0.73 | 72 | empty |
| 5 | 394 | 0.55 | 0.73 | 61 | empty |
Interfaces
6 interfaces between chains.
- C–D · 171 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 171 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 170 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 170 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 108 modified (engineered).
Compared structures
- 4D2U · Negative-stain electron microscopy of E. coli ClpB (BAP form bound to ClpP) · the same entry in another collection · chain F against F, TM-score 1.00
- P63284 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P63284) · a predicted model of the same protein · chain A against A, TM-score 0.57
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 P63284
- Elsewhere: RCSB PDB 4D2U · PDBe 4D2U · UniProt P63284
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