Research workbench
Activated ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) complexed with the reaction intermediate analogue 2-carboxyarabinitol 1,5-bisphosphate
Analyse Activated ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BWV
- Type
- protein
- Length
- 2,440 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (ribulose bisphosphate carboxylase)
- EC
- 4.1.1.39
- UniProt
- O98949, O98950
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Protein (ribulose bisphosphate carboxylase) (EC 4.1.1.39) | protein | 472 | 42% helix, 17% strand | O98949 |
| S, U, W, Y | Protein (ribulose bisphosphate carboxylase) (EC 4.1.1.39) | protein | 138 | 25% helix, 30% strand | O98950 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.76 | 0.96 | 24 | empty |
| 2 | 108 | 0.75 | 0.95 | 26 | empty |
| 3 | 109 | 0.74 | 0.95 | 26 | empty |
| 4 | 615 | 0.74 | 0.81 | 79 | empty |
| 5 | 544 | 0.74 | 0.82 | 70 | empty |
Interfaces
20 interfaces between chains.
- A–S · 1633 Ų buried · 23 hydrogen bonds · protein-protein
- G–Y · 1628 Ų buried · 21 hydrogen bonds · protein-protein
- C–U · 1619 Ų buried · 21 hydrogen bonds · protein-protein
- E–W · 1615 Ų buried · 22 hydrogen bonds · protein-protein
- S–U · 726 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 1BWV · Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the… · the same entry in another collection · chain C against C, 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 O98949
- Every structure of UniProt O98950
- Elsewhere: RCSB PDB 1BWV · PDBe 1BWV · UniProt O98949 · UniProt O98950
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