MolNFT v1 · #79850 · protein
Dmsp-dependent demethylase from P. ubique - with substrate dmsp
3TFI · Gcvt-like aminomethyltransferase protein: “Dmsp-dependent demethylase from P. ubique - with substrate dmsp”. X-ray diffraction, 2 ligands (DQY, NA), 5 pockets (best druggability 0.79). MolNFT v1 #79850 on GenesisL1: 3D structure…
- PDB
- 3TFI
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gcvt-like aminomethyltransferase protein
- EC
- 2.1.2.10
- UniProt
- Q4FP21
- Ligands
- DQY, NA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gcvt-like aminomethyltransferase protein (EC 2.1.2.10) | protein | 369 | 24% helix, 34% strand | Q4FP21 |
Ligands and binding sites
- DQY · 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 774 | 0.79 | 0.83 | 89 | DQY |
| 2 | 868 | 0.79 | 0.81 | 92 | DQY |
| 3 | 343 | 0.66 | 0.81 | 40 | GOL |
| 4 | 340 | 0.65 | 0.80 | 40 | GOL |
| 5 | 52 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2380 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3TFI · DMSP-dependent demethylase from P. ubique - with substrate DMSP · the same entry in another collection · chain A against A, TM-score 1.00
- Q4FP21 · AlphaFold monomer V2.0 prediction for dimethylsulfonioproprionate demethylase dmda… · 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 Q4FP21
- Elsewhere: RCSB PDB 3TFI · PDBe 3TFI · UniProt Q4FP21
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