MolNFT v1 · #155152 · protein
Rice rubisco in complex with sulfate ions
6KYI · Ribulose bisphosphate carboxylase large chain: “Rice rubisco in complex with sulfate ions”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.75). MolNFT v1 #155152 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KYI
- Type
- protein
- Length
- 1,108 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
- P0C510, Q0INY7
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.75
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 | 431 | 45% helix, 18% strand | P0C510 |
| S | Ribulose bisphosphate carboxylase small chain, chloroplastic (EC 4.1.1.39) | protein | 119 | 23% helix, 24% strand | Q0INY7 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 438 | 46% helix, 18% strand | P0C510 |
| T | Ribulose bisphosphate carboxylase small chain, chloroplastic (EC 4.1.1.39) | protein | 120 | 23% helix, 24% strand | Q0INY7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.75 | 0.80 | 59 | SO4 |
| 2 | 72 | 0.75 | 0.98 | 21 | GOL |
| 3 | 729 | 0.71 | 0.78 | 66 | SO4 |
| 4 | 149 | 0.50 | 0.79 | 27 | empty |
| 5 | 211 | 0.50 | 0.76 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3390 Ų buried · 66 hydrogen bonds · protein-protein
- B–T · 1885 Ų buried · 23 hydrogen bonds · protein-protein
- A–S · 1875 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6KYI · Rice Rubisco in complex with sulfate ions · the same entry in another collection · chain T against T, TM-score 1.00
- P0C510 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain A 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 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 P0C510
- Every structure of UniProt Q0INY7
- Elsewhere: RCSB PDB 6KYI · PDBe 6KYI · UniProt P0C510 · UniProt Q0INY7
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