MolNFT v1 · #57224 · protein
Crystal structure of type III rubisco complexed with 2-cabp
3A12 · Ribulose bisphosphate carboxylase: “Crystal structure of type III rubisco complexed with 2-cabp”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.64). MolNFT v1 #57224 on GenesisL1: 3D structure, binding…
- PDB
- 3A12
- Type
- protein
- Length
- 4,366 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 0.64
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, J | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 437 | 42% helix, 17% strand | O93627 |
| B, C | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 438 | 43% helix, 17% strand | O93627 |
| D, G, I | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 436 | 42% helix, 17% strand | O93627 |
| E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 436 | 42% helix, 17% strand | O93627 |
| F | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 435 | 43% 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 · 10 copies · chains A, B, C, D, E, F, G, H, I, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.64 | 0.83 | 47 | CAP |
| 2 | 257 | 0.64 | 0.82 | 52 | MG, CAP |
| 3 | 265 | 0.64 | 0.81 | 50 | MG, CAP |
| 4 | 257 | 0.62 | 0.81 | 52 | MG, CAP |
| 5 | 249 | 0.62 | 0.81 | 51 | MG, CAP |
Interfaces
12 interfaces between chains.
- B–C · 287 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 277 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 269 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 268 Ų buried · 4 hydrogen bonds · protein-protein
- F–J · 267 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (carboxylation).
Compared structures
- 3A12 · Crystal structure of Type III Rubisco 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 E 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 3A12 · PDBe 3A12 · UniProt O93627
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