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Dmsp-dependent demethylase from P. ubique - apo

Analyse Dmsp-dependent demethylase from P. ubique - apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TFH
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: NA
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Gcvt-like aminomethyltransferase protein (EC 2.1.2.10)	protein	369	24% helix, 33% strand	Q4FP21

Ligands and binding sites

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

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	877	0.78	0.81	88	empty
2	771	0.78	0.82	77	empty
3	329	0.65	0.81	40	GOL
4	359	0.65	0.80	43	GOL

Interfaces

1 interface between chains.

A–B · 2402 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

3TFH · DMSP-dependent demethylase from P. ubique - apo · 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 3TFH · PDBe 3TFH · UniProt Q4FP21

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