Research workbench
Crystal structure of activated rice rubisco complexed with 2- carboxyarabinitol-1,5-bisphosphate
Analyse Crystal structure of activated rice rubisco complexed with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WDD
- Type
- protein
- Length
- 1,173 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
- CAP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 465 | 44% helix, 17% strand | P0C512 |
| S, W | Ribulose bisphosphate carboxylase small chain C (EC 4.1.1.39) | protein | 122 | 22% helix, 24% strand | Q0INY7 |
| E | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 464 | 44% helix, 17% strand | P0C512 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 2 copies · chains A, E
- MG · Magnesium ion · metal · 2 copies · chains A, E
- GOL · Glycerol · additive · 17 copies · chains A, E, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.82 | 0.98 | 47 | MG, CAP, GOL |
| 2 | 86 | 0.75 | 0.98 | 32 | MG, CAP |
| 3 | 81 | 0.74 | 0.97 | 19 | empty |
| 4 | 59 | 0.73 | 0.98 | 19 | GOL |
| 5 | 175 | 0.68 | 0.87 | 35 | GOL |
Interfaces
3 interfaces between chains.
- A–E · 4771 Ų buried · 88 hydrogen bonds · protein-protein
- A–S · 1983 Ų buried · 27 hydrogen bonds · protein-protein
- E–W · 1951 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation, nonstandard).
Compared structures
- 1WDD · Crystal Structure of Activated Rice Rubisco Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0C512 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain E against A, TM-score 1.00
- 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 1.00
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 1WDD · PDBe 1WDD · UniProt P0C512 · UniProt Q0INY7
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