Research workbench
Crystal structure of rlmh in complex with sinefungin
Analyse Crystal structure of rlmh in complex with sinefungin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TWK
- 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
- SFG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% 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 | 44% helix, 22% strand | B7MFQ9 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.82 | 0.84 | 70 | SFG |
| 2 | 364 | 0.64 | 0.79 | 47 | SFG |
| 3 | 307 | 0.62 | 0.79 | 38 | SFG |
| 4 | 153 | 0.61 | 0.84 | 23 | SFG |
| 5 | 148 | 0.42 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1241 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1113 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 341 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 337 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5TWK · Crystal Structure of RlmH in Complex with Sinefungin · 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 5TWK · PDBe 5TWK · UniProt B7MFQ9
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