Research workbench
Ribosomal protein L11 methyltransferase (prma) in complex with dimethylated ribosomal protein L11
Analyse Ribosomal protein L11 methyltransferase (prma) in complex with dimethylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CJT
- Type
- protein
- Length
- 2,817 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein L11 methyltransferase; 50S ribosomal protein L11
- EC
- 2.1.1.-
- UniProt
- Q84BQ9, P36238
- Ligands
- SAH, 2MM, SAM, NO3, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Ribosomal protein L11 methyltransferase (EC 2.1.1.-) | protein | 254 | 33% helix, 32% strand | Q84BQ9 |
| B | 50S ribosomal protein L11 | protein | 126 | 30% helix, 19% strand | P36238 |
| C, K, O | Ribosomal protein L11 methyltransferase (EC 2.1.1.-) | protein | 250 | 32% helix, 32% strand | Q84BQ9 |
| D, L, P | 50S ribosomal protein L11 | protein | 72 | 24% helix, 33% strand | P36238 |
| F, N | 50S ribosomal protein L11 | protein | 130 | 29% helix, 18% strand | P36238 |
| G | Ribosomal protein L11 methyltransferase (EC 2.1.1.-) | protein | 251 | 32% helix, 32% strand | Q84BQ9 |
| H | 50S ribosomal protein L11 | protein | 71 | 24% helix, 34% strand | P36238 |
| J | 50S ribosomal protein L11 | protein | 127 | 30% helix, 19% strand | P36238 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, E, F, I, J, M, N
- 2MM · N,N-dimethyl-L-methionine · ligand · 4 copies · chains A, B, E, F, I, J, M, N
- SAM · S-adenosylmethionine · ligand · 4 copies · chains C, G, K, O
- NO3 · Nitrate ion · ion · 8 copies · chains A, B, E, F, I, J, M, N
- CL · Chloride ion · ion · 4 copies · chains A, E, I, M
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 826 | 0.87 | 0.89 | 98 | empty |
| 2 | 378 | 0.82 | 0.91 | 44 | empty |
| 3 | 970 | 0.71 | 0.76 | 88 | empty |
| 4 | 695 | 0.70 | 0.77 | 57 | empty |
| 5 | 646 | 0.69 | 0.77 | 59 | empty |
Interfaces
30 interfaces between chains.
- M–N · 1690 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1688 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1679 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1673 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 939 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3CJT · Ribosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal… · the same entry in another collection · chain H against H, 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 Q84BQ9
- Every structure of UniProt P36238
- Elsewhere: RCSB PDB 3CJT · PDBe 3CJT · UniProt Q84BQ9 · UniProt P36238
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.