MolNFT v1 · #171333 · protein
Crystal structure of the aaa domain of rubisco activase from nostoc sp. (strain pcc 7120), gadolinium complex
6Z1D · Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase: “Crystal structure of the aaa domain of rubisco activase from nostoc sp. (strain pcc 7120), gadolinium complex”. X-ray diffraction, 3 ligands (ADP, GD, CL), 5 pockets (best…
- 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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