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Sdea mart-C domain EE/AA apo

Analyse Sdea mart-C domain EE/AA apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YSK
Type: protein
Length: 550 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UBIQUITINATING/DEUBIQUITINATING enzyme sdea
EC: 3.4.22.-
UniProt: Q5ZTK4
Pockets: 7 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-)	protein	137	31% helix, 34% strand	Q5ZTK4
B	UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-)	protein	135	31% helix, 33% strand	Q5ZTK4
C	UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-)	protein	135	31% helix, 36% strand	Q5ZTK4
D	UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-)	protein	143	30% helix, 32% strand	Q5ZTK4

Pockets

7 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	538	0.66	0.77	58	empty
2	377	0.62	0.78	46	empty
3	155	0.46	0.76	19	empty
4	136	0.46	0.77	19	empty
5	132	0.44	0.76	18	empty

Interfaces

4 interfaces between chains.

A–C · 1016 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 982 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 271 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 203 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

5YSK · SdeA mART-C domain EE/AA apo · the same entry in another collection · chain D against D, TM-score 1.00
Q5ZTK4 · AlphaFold monomer V2.0 prediction for UBIQUITINATING/DEUBIQUITINATING enzyme sdea (Q5ZTK4) · a predicted model of the same protein · chain B against A, TM-score 0.84

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 Q5ZTK4
Elsewhere: RCSB PDB 5YSK · PDBe 5YSK · UniProt Q5ZTK4

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