MolNFT v1 · #75605 · protein
Crystal structure of apo mnmc from yersinia pestis
3PVC · TRNA 5-methylaminomethyl-2-thiouridine biosynthesis…: “Crystal structure of apo mnmc from yersinia pestis”. X-ray diffraction, 2 ligands (FAD, CL), 7 pockets (best druggability 0.82). MolNFT v1 #75605 on GenesisL1: 3D structure…
- PDB
- 3PVC
- Type
- protein
- Length
- 635 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.-, 1.5.-.-
- UniProt
- Q8ZD36
- Ligands
- FAD, CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmc (EC 2.1.1.-, 1.5.-.-) | protein | 635 | 34% helix, 24% strand | Q8ZD36 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.82 | 0.84 | 93 | FAD, CL |
| 2 | 309 | 0.58 | 0.77 | 39 | empty |
| 3 | 235 | 0.54 | 0.77 | 38 | empty |
| 4 | 141 | 0.48 | 0.78 | 19 | empty |
| 5 | 74 | 0.46 | 0.82 | 23 | empty |
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3PVC · Crystal structure of apo MnmC from Yersinia Pestis · 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 0.99
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 3PVC · PDBe 3PVC · UniProt Q8ZD36
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