Research workbench
Negative stain EM MAP of the aaa protein cbbx, a red-type rubisco activase from R. sphaeroides
Analyse Negative stain EM MAP of the aaa protein cbbx, a red-type rubisco activase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZUH
- Type
- protein
- Length
- 1,716 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein cbbx
- UniProt
- P95648
- Ligands
- RUB, ADP
- Pockets
- 19 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protein cbbx | protein | 286 | 54% helix, 11% strand | P95648 |
Ligands and binding sites
- RUB · Ribulose-1,5-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.84 | 0.85 | 123 | empty |
| 2 | 969 | 0.78 | 0.80 | 100 | ADP |
| 3 | 930 | 0.78 | 0.80 | 97 | ADP |
| 4 | 858 | 0.77 | 0.81 | 93 | ADP |
| 5 | 913 | 0.77 | 0.80 | 100 | ADP |
Interfaces
6 interfaces between chains.
- C–D · 1484 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1476 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1475 Ų buried · 31 hydrogen bonds · protein-protein
- A–F · 1473 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1470 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 3ZUH · Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R.… · the same entry in another collection · chain F against F, TM-score 1.00
- P95648 · AlphaFold monomer V2.0 prediction for protein cbbx (P95648) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P95648
- Elsewhere: RCSB PDB 3ZUH · PDBe 3ZUH · UniProt P95648
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