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The carboxyl terminal domain of human deltex 3-like

Analyse The carboxyl terminal domain of human deltex 3-like in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PG6
Type: protein
Length: 538 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase DTX3L
EC: 6.3.2.-
UniProt: Q8TDB6
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	E3 ubiquitin-protein ligase DTX3L (EC 6.3.2.-)	protein	135	21% helix, 32% strand	Q8TDB6
B, D	E3 ubiquitin-protein ligase DTX3L (EC 6.3.2.-)	protein	134	22% helix, 31% strand	Q8TDB6

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
CIT · Citric acid · additive · 3 copies · chains A, D, B, C
GOL · Glycerol · additive · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1066	0.83	0.84	101	CIT, GOL
2	545	0.73	0.81	53	CIT
3	127	0.41	0.76	19	empty
4	59	0.28	0.73	19	empty

Interfaces

6 interfaces between chains.

A–D · 1159 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1152 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 577 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 228 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 140 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3PG6 · The carboxyl terminal domain of human deltex 3-like · the same entry in another collection · chain D against D, TM-score 1.00
Q8TDB6 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase DTX3L (Q8TDB6) · a predicted model of the same protein · chain D 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 Q8TDB6
Elsewhere: RCSB PDB 3PG6 · PDBe 3PG6 · UniProt Q8TDB6

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