Research workbench
The crystal structure of mnmc from yersinia pestis bound with FAD and SAM
Analyse The crystal structure of mnmc from yersinia pestis bound with FAD and SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SGL
- Type
- protein
- Length
- 630 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmc
- EC
- 2.1.1.61, 1.5.-.-
- UniProt
- Q8ZD36
- Ligands
- FAD, SAM, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmc (EC 2.1.1.61, 1.5.-.-) | protein | 630 | 34% helix, 25% strand | Q8ZD36 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.81 | 0.84 | 94 | FAD, CL |
| 2 | 289 | 0.59 | 0.78 | 40 | SAM |
| 3 | 155 | 0.49 | 0.78 | 19 | empty |
| 4 | 118 | 0.44 | 0.77 | 26 | empty |
| 5 | 125 | 0.43 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3SGL · The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZD36 · AlphaFold monomer V2.0 prediction for tRNA 5-methylaminomethyl-2-thiouridine biosynthesis… · a predicted model of the same protein · 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 Q8ZD36
- Elsewhere: RCSB PDB 3SGL · PDBe 3SGL · UniProt Q8ZD36
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