MolNFT v1 · #1213 · protein
Activated unliganded spinach rubisco
1AUS · Ribulose bisphosphate CARBOXYLASE/OXYGENASE: “Activated unliganded spinach rubisco”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.64). MolNFT v1 #1213 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1AUS
- Type
- protein
- Length
- 2,248 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate CARBOXYLASE/OXYGENASE
- EC
- 4.1.1.39
- UniProt
- P00875, Q43832
- Ligands
- MG
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M, N, O | Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 439 | 46% helix, 18% strand | P00875 |
| S, T, U, V | Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 123 | 23% helix, 24% strand | Q43832 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains L, M, N, O
- FMT · Formic acid · additive · 4 copies · chains L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.64 | 0.76 | 68 | empty |
| 2 | 261 | 0.63 | 0.81 | 29 | empty |
| 3 | 373 | 0.63 | 0.78 | 58 | empty |
| 4 | 345 | 0.62 | 0.78 | 55 | empty |
| 5 | 235 | 0.62 | 0.81 | 31 | empty |
Interfaces
16 interfaces between chains.
- M–T · 1928 Ų buried · 25 hydrogen bonds · protein-protein
- L–S · 1926 Ų buried · 25 hydrogen bonds · protein-protein
- N–U · 1925 Ų buried · 25 hydrogen bonds · protein-protein
- O–V · 1925 Ų buried · 25 hydrogen bonds · protein-protein
- L–V · 1038 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 1AUS · Activated unliganded spinach rubisco · the same entry in another collection · chain V against V, TM-score 1.00
- P00875 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain L against A, TM-score 0.99
- Q43832 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain S against A, TM-score 0.98
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 P00875
- Every structure of UniProt Q43832
- Elsewhere: RCSB PDB 1AUS · PDBe 1AUS · UniProt P00875 · UniProt Q43832
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