Research workbench
Crystal structure of the aaa domain of rubisco activase from nostoc sp. (strain pcc 7120), gadolinium complex
Analyse Crystal structure of the aaa domain of rubisco activase from nostoc sp. (strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z1D
- 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, GD, CL
- Pockets
- 5 · best druggability 0.78
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 | 55% helix, 10% strand | P58555 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- GD · Gadolinium atom · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
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 | 1044 | 0.78 | 0.80 | 66 | ADP, GD |
| 2 | 169 | 0.50 | 0.78 | 21 | empty |
| 3 | 65 | 0.39 | 0.79 | 14 | empty |
| 4 | 86 | 0.36 | 0.76 | 19 | empty |
| 5 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1410 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6Z1D · Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC… · 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 6Z1D · PDBe 6Z1D · UniProt P58555
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