MolNFT v1 · #138736 · protein
Structure of ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE from wheat
5WSK · Ribulose bisphosphate carboxylase large chain: “Structure of ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE from wheat”. X-ray diffraction, 1 ligand (MG), 19 pockets (best druggability 0.80). MolNFT v1 #138736 on GenesisL1: 3D…
- PDB
- 5WSK
- Type
- protein
- Length
- 2,246 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
- P11383, W5F0E6
- Ligands
- MG
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 441 | 45% helix, 18% strand | P11383 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 439 | 44% helix, 18% strand | P11383 |
| C | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 440 | 45% helix, 18% strand | P11383 |
| D | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 440 | 45% helix, 18% strand | P11383 |
| E, F, G | Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) | protein | 122 | 22% helix, 24% strand | W5F0E6 |
| H | Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) | protein | 120 | 23% helix, 24% strand | W5F0E6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.80 | 0.84 | 64 | MG |
| 2 | 87 | 0.78 | 0.99 | 22 | empty |
| 3 | 979 | 0.78 | 0.80 | 68 | empty |
| 4 | 758 | 0.75 | 0.80 | 65 | MG |
| 5 | 733 | 0.75 | 0.81 | 60 | MG |
Interfaces
9 interfaces between chains.
- A–B · 3701 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 3683 Ų buried · 60 hydrogen bonds · protein-protein
- A–E · 1923 Ų buried · 23 hydrogen bonds · protein-protein
- B–F · 1892 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 1886 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (carboxylation, disulfide).
Compared structures
- 5WSK · Structure of Ribulose-1,5-bisphosphate carboxylase/oxygenase from wheat · the same entry in another collection · chain G against G, TM-score 1.00
- P11383 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P11383
- Every structure of UniProt W5F0E6
- Elsewhere: RCSB PDB 5WSK · PDBe 5WSK · UniProt P11383 · UniProt W5F0E6
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