Research workbench
Crystal structure of type III rubisco SP6 mutant complexed with 2-cabp
Analyse Crystal structure of type III rubisco SP6 mutant complexed with 2-cabp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDO
- Type
- protein
- Length
- 4,379 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- O93627
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 436 | 41% helix, 18% strand | O93627 |
| B, H, I, J | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 438 | 41% helix, 18% strand | O93627 |
| C, E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 440 | 42% helix, 18% strand | O93627 |
| D, F, G | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 437 | 42% helix, 18% strand | O93627 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 10 copies · chains A, H, B, G, C, F, D, J, E, I
- MG · Magnesium ion · metal · 10 copies · chains A, H, B, G, C, F, D, J, E, I
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 | 105 | 0.80 | 0.98 | 33 | empty |
| 2 | 105 | 0.79 | 0.98 | 34 | empty |
| 3 | 102 | 0.79 | 0.98 | 33 | empty |
| 4 | 101 | 0.79 | 0.98 | 32 | empty |
| 5 | 95 | 0.79 | 0.98 | 30 | empty |
Interfaces
20 interfaces between chains.
- C–F · 4511 Ų buried · 74 hydrogen bonds · protein-protein
- B–G · 4506 Ų buried · 77 hydrogen bonds · protein-protein
- D–J · 4501 Ų buried · 76 hydrogen bonds · protein-protein
- E–I · 4465 Ų buried · 70 hydrogen bonds · protein-protein
- A–H · 4363 Ų buried · 73 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (carboxylation).
Compared structures
- 3KDO · Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP · the same entry in another collection · chain J against J, TM-score 1.00
- O93627 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (O93627) · a predicted model of the same protein · chain C 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 O93627
- Elsewhere: RCSB PDB 3KDO · PDBe 3KDO · UniProt O93627
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