Research workbench
Crystal structure of the complex of sulfate ion and octameric ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) from pyrococcus horikoshii OT3 (form-2 crystal)
Analyse Crystal structure of the complex of sulfate ion and octameric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D69
- Type
- protein
- Length
- 1,671 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
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 424 | 44% helix, 18% strand | O58677 |
| B | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 418 | 45% helix, 18% strand | O58677 |
| D | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 419 | 44% helix, 18% strand | O58677 |
| E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 410 | 44% helix, 18% strand | O58677 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 19 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.79 | 0.82 | 70 | SO4 |
| 2 | 950 | 0.78 | 0.81 | 69 | SO4 |
| 3 | 66 | 0.76 | 0.99 | 23 | empty |
| 4 | 471 | 0.65 | 0.78 | 46 | empty |
| 5 | 456 | 0.63 | 0.76 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–E · 3509 Ų buried · 53 hydrogen bonds · protein-protein
- D–E · 701 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 396 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2D69 · Crystal structure of the complex of sulfate ion and octameric ribulose-1,5-bisphosphate… · the same entry in another collection · chain E against E, TM-score 1.00
- O58677 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (O58677) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 2D69 · PDBe 2D69 · UniProt O58677
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