Research workbench
Crystal structure of type III rubisco SP4 mutant complexed with 2-cabp and activated with ca
Analyse Crystal structure of type III rubisco SP4 mutant complexed with 2-cabp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A13
- Type
- protein
- Length
- 4,362 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, CA
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 436 | 42% helix, 17% strand | O93627 |
| B, F, G | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 437 | 41% helix, 17% strand | O93627 |
| C | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 437 | 41% helix, 17% strand | O93627 |
| D, I | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 437 | 42% helix, 17% strand | O93627 |
| E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 432 | 41% helix, 17% strand | O93627 |
| H | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 438 | 41% helix, 17% strand | O93627 |
| J | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 434 | 41% helix, 17% strand | O93627 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, F, G, H, I
- CA · Calcium ion · metal · 2 copies · chains E, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.64 | 0.80 | 56 | MG, CAP |
| 2 | 300 | 0.64 | 0.81 | 56 | MG, CAP |
| 3 | 325 | 0.63 | 0.80 | 53 | MG, CAP |
| 4 | 311 | 0.61 | 0.79 | 53 | CAP |
| 5 | 256 | 0.61 | 0.80 | 48 | MG, CAP |
Interfaces
14 interfaces between chains.
- I–J · 280 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 277 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 271 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 270 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (carboxylation).
Compared structures
- 3A13 · Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP and activated with… · 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 B 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 3A13 · PDBe 3A13 · UniProt O93627
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