Research workbench
Mtb clpb in complex with atpgammas and casein, conformer 2
Analyse Mtb clpb in complex with atpgammas and casein, conformer 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DJV
- Type
- protein
- Length
- 3,530 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Casein polyalanine model
- UniProt
- A0A045JSR5
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein clpb | protein | 610 | 44% helix, 9% strand | A0A045JSR5 |
| B | Chaperone protein clpb | protein | 611 | 42% helix, 11% strand | A0A045JSR5 |
| C | Chaperone protein clpb | protein | 615 | 40% helix, 10% strand | A0A045JSR5 |
| D | Chaperone protein clpb | protein | 562 | 38% helix, 9% strand | A0A045JSR5 |
| N | Casein polyalanine model | protein | 26 | 0% helix, 15% strand | — |
| E | Chaperone protein clpb | protein | 548 | 36% helix, 9% strand | A0A045JSR5 |
| F | Chaperone protein clpb | protein | 558 | 38% helix, 11% strand | A0A045JSR5 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 10 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1095 | 0.86 | 0.87 | 133 | AGS |
| 2 | 837 | 0.85 | 0.88 | 109 | AGS |
| 3 | 1033 | 0.85 | 0.86 | 101 | AGS |
| 4 | 1196 | 0.84 | 0.85 | 107 | AGS |
| 5 | 691 | 0.84 | 0.88 | 75 | AGS |
Interfaces
16 interfaces between chains.
- B–C · 4301 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 4248 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 4227 Ų buried · 56 hydrogen bonds · protein-protein
- A–F · 3906 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2222 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6DJV · Mtb ClpB in complex with ATPgammaS and casein, Conformer 2 · the same entry in another collection · chain C against C, 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 A0A045JSR5
- Elsewhere: RCSB PDB 6DJV · PDBe 6DJV · UniProt A0A045JSR5
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