Research workbench
Mtb clpb in complex with atpgammas and casein, conformer 1
Analyse Mtb clpb in complex with atpgammas and casein, conformer 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DJU
- Type
- protein
- Length
- 3,502 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 0.87
Structure
electron microscopy · 7 distinct chains · 40% helix, 9% 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 | 41% helix, 10% strand | A0A045JSR5 |
| C | Chaperone protein clpb | protein | 614 | 42% 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 | 39% helix, 7% strand | A0A045JSR5 |
| F | Chaperone protein clpb | protein | 531 | 39% helix, 8% 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, F
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 | 920 | 0.87 | 0.89 | 134 | ADP |
| 2 | 1157 | 0.86 | 0.87 | 130 | AGS |
| 3 | 798 | 0.85 | 0.88 | 102 | empty |
| 4 | 1140 | 0.84 | 0.85 | 103 | AGS |
| 5 | 276 | 0.84 | 0.94 | 45 | empty |
Interfaces
14 interfaces between chains.
- B–C · 4349 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 4217 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4076 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2202 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1728 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6DJU · Mtb ClpB in complex with ATPgammaS and casein, Conformer 1 · 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 A0A045JSR5
- Elsewhere: RCSB PDB 6DJU · PDBe 6DJU · UniProt A0A045JSR5
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