MolNFT v1 · #171334 · protein
Crystal structure of the aaa domain of rubisco activase from nostoc sp. (strain pcc 7120)
6Z1E · Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase: “Crystal structure of the aaa domain of rubisco activase from nostoc sp. (strain pcc 7120)”. X-ray diffraction, 2 ligands (ADP, CL), 5 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 6Z1E
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase
- UniProt
- P58555
- Ligands
- ADP, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase | protein | 274 | 50% helix, 10% strand | P58555 |
| B | Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase | protein | 259 | 54% helix, 10% strand | P58555 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
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 | 1114 | 0.77 | 0.79 | 73 | ADP |
| 2 | 166 | 0.47 | 0.76 | 22 | empty |
| 3 | 85 | 0.37 | 0.76 | 17 | empty |
| 4 | 63 | 0.36 | 0.78 | 14 | empty |
| 5 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1328 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6Z1E · Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120) · the same entry in another collection · chain A against A, TM-score 1.00
- P58555 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate CARBOXYLASE/OXYGENASE… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P58555
- Elsewhere: RCSB PDB 6Z1E · PDBe 6Z1E · UniProt P58555
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