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A crystal form of ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase from nicotiana tabacum in the activated state
Analyse A crystal form of ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RUB
- Type
- protein
- Length
- 2,348 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE (form IV)
- EC
- 4.1.1.39
- UniProt
- P00876, P69249
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE (form IV) (EC 4.1.1.39) | protein | 464 | 45% helix, 17% strand | P00876 |
| S, T, U, V | Ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE (form IV) (EC 4.1.1.39) | protein | 123 | 21% helix, 24% strand | P69249 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, D, B, C
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.78 | 0.97 | 25 | empty |
| 2 | 121 | 0.78 | 0.97 | 26 | empty |
| 3 | 111 | 0.78 | 0.97 | 24 | empty |
| 4 | 1051 | 0.77 | 0.79 | 77 | empty |
| 5 | 356 | 0.76 | 0.87 | 62 | MG, CAP |
Interfaces
15 interfaces between chains.
- B–C · 4723 Ų buried · 89 hydrogen bonds · protein-protein
- A–D · 4703 Ų buried · 93 hydrogen bonds · protein-protein
- B–T · 1869 Ų buried · 25 hydrogen bonds · protein-protein
- D–V · 1863 Ų buried · 25 hydrogen bonds · protein-protein
- C–U · 1857 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent (disulfide, additive adduct).
Compared structures
- 4RUB · A crystal form of ribulose-1,5-bisphosphate CARBOXYLASE(SLASH)OXYGENASE from nicotiana… · the same entry in another collection · chain V against V, TM-score 1.00
- P00876 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P69249 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain S 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 P00876
- Every structure of UniProt P69249
- Elsewhere: RCSB PDB 4RUB · PDBe 4RUB · UniProt P00876 · UniProt P69249
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