Research workbench
Structure of rubisco lsmt bound to sinefungin and monomethyllysine
Analyse Structure of rubisco lsmt bound to sinefungin and monomethyllysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H2J
- Type
- protein
- Length
- 1,300 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
- SFG, MLZ
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 11% 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 | 423 | 48% helix, 10% strand | Q43088 |
| B | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 439 | 46% helix, 12% strand | Q43088 |
| C | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 438 | 45% helix, 11% strand | Q43088 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 3 copies · chains A, B, C
- MLZ · N-methyl-lysine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.80 | 0.82 | 92 | empty |
| 2 | 609 | 0.74 | 0.81 | 76 | SFG, MLZ |
| 3 | 547 | 0.74 | 0.81 | 51 | SFG, MLZ |
| 4 | 597 | 0.72 | 0.80 | 52 | SFG, MLZ |
| 5 | 227 | 0.49 | 0.74 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1432 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1423 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1356 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2H2J · Structure of Rubisco LSMT bound to Sinefungin and Monomethyllysine · the same entry in another collection · chain B against B, 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 2H2J · PDBe 2H2J · UniProt Q43088
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