Research workbench
Aaa+ ATPase, clpl from streptococcus pneumoniae: atprs-bound
Analyse Aaa+ ATPase, clpl from streptococcus pneumoniae: atprs-bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LT4
- Type
- protein
- Length
- 8,722 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease, ATP-binding subunit
- UniProt
- A0A0H2ZMB9
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | ATP-dependent clp protease, ATP-binding subunit | protein | 623 | 50% helix, 12% strand | A0A0H2ZMB9 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- MG · Magnesium ion · metal · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 279 | 0.84 | 0.94 | 38 | empty |
| 2 | 853 | 0.84 | 0.86 | 107 | AGS, MG |
| 3 | 273 | 0.83 | 0.94 | 38 | empty |
| 4 | 266 | 0.83 | 0.94 | 37 | empty |
| 5 | 268 | 0.83 | 0.94 | 38 | empty |
Interfaces
21 interfaces between chains.
- D–E · 2156 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2145 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 2139 Ų buried · 25 hydrogen bonds · protein-protein
- H–N · 2129 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2121 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6LT4 · AAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound · 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 A0A0H2ZMB9
- Elsewhere: RCSB PDB 6LT4 · PDBe 6LT4 · UniProt A0A0H2ZMB9
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