MolNFT v1 · #38572 · protein
Structure of rubisco lsmt bound to azaadomet and lysine
2H2E · Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large…: “Structure of rubisco lsmt bound to azaadomet and lysine”. X-ray diffraction, 2 ligands (SA8, LYS), 18 pockets (best druggability 0.79). MolNFT v1 #38572 on GenesisL1: 3D…
- PDB
- 2H2E
- Type
- protein
- Length
- 1,302 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase
- EC
- 2.1.1.127
- UniProt
- Q43088
- Ligands
- SA8, LYS
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 424 | 46% helix, 11% strand | Q43088 |
| B | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 440 | 47% helix, 11% strand | Q43088 |
| C | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 438 | 45% helix, 12% strand | Q43088 |
Ligands and binding sites
- SA8 · S-5'-azamethionine-5'-deoxyadenosine · ligand · 3 copies · chains A, B, C
- LYS · Lysine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.79 | 0.82 | 72 | empty |
| 2 | 662 | 0.75 | 0.81 | 62 | SA8, LYS |
| 3 | 637 | 0.73 | 0.80 | 53 | SA8, LYS |
| 4 | 574 | 0.71 | 0.79 | 55 | SA8, LYS |
| 5 | 235 | 0.50 | 0.75 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1432 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1398 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1363 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2H2E · Structure of Rubisco LSMT bound to AzaAdoMet and Lysine · the same entry in another collection · chain A against A, TM-score 1.00
- Q43088 · AlphaFold monomer V2.0 prediction for ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q43088
- Elsewhere: RCSB PDB 2H2E · PDBe 2H2E · UniProt Q43088
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.