Research workbench
Hybrid-rubisco (rice rbcl and sorghum rbcs) in complex with sulfate ions
Analyse Hybrid-rubisco (rice rbcl and sorghum rbcs) in complex with sulfate ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KYJ
- Type
- protein
- Length
- 2,275 residues
- Chains
- 8
- 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, E3WDK7
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 448 | 45% helix, 19% strand | P0C510 |
| S | Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) | protein | 119 | 23% helix, 24% strand | E3WDK7 |
| E | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 450 | 45% helix, 19% strand | P0C510 |
| W, Y | Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) | protein | 120 | 23% helix, 24% strand | E3WDK7 |
| U | Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) | protein | 123 | 22% helix, 24% strand | E3WDK7 |
| G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 447 | 45% helix, 19% strand | P0C510 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, E, C, G
- GOL · Glycerol · additive · 13 copies · chains A, G, S, W, E, U, C, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.66 | 0.80 | 71 | GOL |
| 2 | 349 | 0.63 | 0.79 | 50 | empty |
| 3 | 266 | 0.62 | 0.80 | 53 | GOL |
| 4 | 265 | 0.62 | 0.80 | 32 | empty |
| 5 | 243 | 0.62 | 0.81 | 32 | empty |
Interfaces
16 interfaces between chains.
- C–U · 1962 Ų buried · 23 hydrogen bonds · protein-protein
- E–W · 1958 Ų buried · 21 hydrogen bonds · protein-protein
- A–S · 1954 Ų buried · 24 hydrogen bonds · protein-protein
- G–Y · 1918 Ų buried · 22 hydrogen bonds · protein-protein
- A–W · 1016 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6KYJ · Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfate ions · the same entry in another collection · chain Y against Y, TM-score 1.00
- P0C510 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain G 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 E3WDK7
- Elsewhere: RCSB PDB 6KYJ · PDBe 6KYJ · UniProt P0C510 · UniProt E3WDK7
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