Research workbench
X-ray crystal structure of C118A rlmn from escherichia COLI with S- adenosylmethionine
Analyse X-ray crystal structure of C118A rlmn from escherichia COLI with S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PL1
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual-specificity RNA methyltransferase rlmn
- EC
- 2.1.1.192
- UniProt
- C9QPQ6
- Ligands
- SAM, SF4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dual-specificity RNA methyltransferase rlmn (EC 2.1.1.192) | protein | 359 | 40% helix, 19% strand | C9QPQ6 |
| A | Dual-specificity RNA methyltransferase rlmn (EC 2.1.1.192) | protein | 332 | 39% helix, 21% strand | C9QPQ6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, A
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.85 | 0.88 | 70 | SAM, SF4 |
| 2 | 1104 | 0.80 | 0.81 | 79 | SAM, SF4 |
| 3 | 328 | 0.51 | 0.73 | 33 | empty |
| 4 | 61 | 0.51 | 0.86 | 18 | empty |
| 5 | 60 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- B–A · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4PL1 · X-ray crystal structure of C118A RlmN from Escherichia coli with S-adenosylmethionine · the same entry in another collection · chain A against A, 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 C9QPQ6
- Elsewhere: RCSB PDB 4PL1 · PDBe 4PL1 · UniProt C9QPQ6
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