Research workbench
Crystal structure of rlmh in complex with S-adenosylmethionine
Analyse Crystal structure of rlmh in complex with S-adenosylmethionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TWJ
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase H
- EC
- 2.1.1.177
- UniProt
- B7MFQ9
- Ligands
- SAM
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B | Ribosomal RNA large subunit methyltransferase H (EC 2.1.1.177) | protein | 157 | 45% helix, 20% strand | B7MFQ9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.80 | 0.83 | 65 | SAM |
| 2 | 404 | 0.64 | 0.78 | 47 | SAM |
| 3 | 382 | 0.62 | 0.77 | 42 | SAM |
| 4 | 161 | 0.58 | 0.82 | 25 | SAM |
| 5 | 142 | 0.43 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1137 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1098 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 435 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 334 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5TWJ · Crystal Structure of RlmH in Complex with S-Adenosylmethionine · the same entry in another collection · chain B against B, TM-score 1.00
- B7MFQ9 · AlphaFold monomer V2.0 prediction for ribosomal RNA large subunit methyltransferase H… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B7MFQ9
- Elsewhere: RCSB PDB 5TWJ · PDBe 5TWJ · UniProt B7MFQ9
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