Research workbench
Crystal structure of octameric ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) from pyrococcus horikoshii OT3 (form- 2 crystal)
Analyse Crystal structure of octameric ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CXE
- Type
- protein
- Length
- 1,664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- O58677
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 416 | 41% helix, 17% strand | O58677 |
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 | 751 | 0.77 | 0.82 | 67 | empty |
| 2 | 776 | 0.77 | 0.81 | 64 | empty |
| 3 | 60 | 0.74 | 0.98 | 25 | empty |
| 4 | 62 | 0.73 | 0.98 | 22 | empty |
| 5 | 549 | 0.64 | 0.76 | 40 | empty |
Interfaces
4 interfaces between chains.
- B–C · 3611 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 661 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 437 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 428 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2CXE · Crystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)… · the same entry in another collection · chain A against A, TM-score 1.00
- O58677 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (O58677) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O58677
- Elsewhere: RCSB PDB 2CXE · PDBe 2CXE · UniProt O58677
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