MolNFT v1 · #122596 · protein
Rubisco from arabidopsis thaliana
5IU0 · Ribulose bisphosphate carboxylase large chain: “Rubisco from arabidopsis thaliana”. X-ray diffraction, 2 ligands (CAP, MG), 19 pockets (best druggability 0.76). MolNFT v1 #122596 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5IU0
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- O03042, P10796
- Ligands
- CAP, MG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 463 | 44% helix, 17% strand | O03042 |
| J, I | Ribulose bisphosphate carboxylase small chain 1B, chloroplastic (EC 4.1.1.39) | protein | 123 | 22% helix, 24% strand | P10796 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, J, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.76 | 0.98 | 29 | MG, CAP |
| 2 | 92 | 0.75 | 0.97 | 35 | CAP |
| 3 | 78 | 0.75 | 0.98 | 18 | empty |
| 4 | 75 | 0.73 | 0.97 | 20 | empty |
| 5 | 163 | 0.67 | 0.87 | 32 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 4745 Ų buried · 90 hydrogen bonds · protein-protein
- A–I · 1956 Ų buried · 28 hydrogen bonds · protein-protein
- B–J · 1932 Ų buried · 26 hydrogen bonds · protein-protein
- A–J · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (carboxylation, disulfide).
Compared structures
- 5IU0 · Rubisco from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- O03042 · 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
- P10796 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit 1B… · a predicted model of the same protein · chain J 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 O03042
- Every structure of UniProt P10796
- Elsewhere: RCSB PDB 5IU0 · PDBe 5IU0 · UniProt O03042 · UniProt P10796
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