Research workbench
Crystal structure of a rubisco-like protein RLP2 from rhodopseudomonas palustris
Analyse Crystal structure of a rubisco-like protein RLP2 from rhodopseudomonas palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QYG
- Type
- protein
- Length
- 1,716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase-like protein 2
- UniProt
- Q6ND47
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribulose bisphosphate carboxylase-like protein 2 | protein | 429 | 42% helix, 18% strand | Q6ND47 |
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.79 | 0.89 | 63 | empty |
| 2 | 318 | 0.78 | 0.89 | 51 | empty |
| 3 | 73 | 0.76 | 0.98 | 23 | empty |
| 4 | 463 | 0.75 | 0.84 | 53 | empty |
| 5 | 453 | 0.74 | 0.83 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3854 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3854 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1155 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 43 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2QYG · Crystal Structure of a RuBisCO-like Protein rlp2 from Rhodopseudomonas palustris · the same entry in another collection · chain A against A, TM-score 1.00
- Q6ND47 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase-like protein 2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6ND47
- Elsewhere: RCSB PDB 2QYG · PDBe 2QYG · UniProt Q6ND47
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