Research workbench
Structure of rice rubisco in complex with NADP(H)
Analyse Structure of rice rubisco in complex with NADP(H) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AXK
- Type
- protein
- Length
- 1,103 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
- P0C512, Q0INY7
- Ligands
- NDP, MG, NME
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 434 | 47% helix, 19% strand | P0C512 |
| S | Ribulose bisphosphate carboxylase small chain, chloroplastic (EC 4.1.1.39) | protein | 120 | 23% helix, 24% strand | Q0INY7 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 430 | 46% helix, 19% strand | P0C512 |
| T | Ribulose bisphosphate carboxylase small chain, chloroplastic (EC 4.1.1.39) | protein | 119 | 23% helix, 24% strand | Q0INY7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NME · Methylamine · ion · 2 copies · chains A, S, B, T
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.76 | 0.98 | 21 | GOL |
| 2 | 704 | 0.69 | 0.77 | 59 | NDP, MG |
| 3 | 652 | 0.67 | 0.76 | 61 | MG, NDP |
| 4 | 179 | 0.50 | 0.78 | 32 | empty |
| 5 | 182 | 0.48 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3201 Ų buried · 62 hydrogen bonds · protein-protein
- A–S · 1902 Ų buried · 21 hydrogen bonds · protein-protein
- B–T · 1885 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 3AXK · Structure of rice Rubisco in complex with NADP(H) · the same entry in another collection · chain T against T, TM-score 1.00
- P0C512 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q0INY7 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain T 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 P0C512
- Every structure of UniProt Q0INY7
- Elsewhere: RCSB PDB 3AXK · PDBe 3AXK · UniProt P0C512 · UniProt Q0INY7
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