MolNFT v1 · #164411 · protein

Structure of active gid E3 ubiquitin ligase complex minus GID2 and delta GID9 ring domain

6SWY · Vacuolar import and degradation protein 28: “Structure of active gid E3 ubiquitin ligase complex minus GID2 and delta GID9 ring domain”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #164411 on GenesisL1: 3D…

PDB: 6SWY
Type: protein
Length: 2,030 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar import and degradation protein 28; Glucose-induced degradation protein 8…
EC: 2.3.2.27
UniProt: P40547, P40208, P53076, P38263, P40492
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 5 distinct chains · 53% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
5	Vacuolar import and degradation protein 28	protein	789	66% helix, 1% strand	P40547
8	Glucose-induced degradation protein 8	protein	325	57% helix, 3% strand	P40208
1	Vacuolar import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30, vacuolar import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30, vacuolar import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degra	protein	542	44% helix, 14% strand	P53076
4	Vacuolar import and degradation protein 24	protein	217	13% helix, 31% strand	P38263
9	Protein FYV10,PROTEIN FYV10,PROTEIN FYV10,PROTEIN FYV10, protein FYV10,PROTEIN FYV10,PROTEIN FYV10 (EC 2.3.2.27)	protein	157	63% helix, 1% strand	P40492

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	910	0.85	0.86	98	empty
2	1123	0.84	0.85	89	empty
3	778	0.75	0.80	76	empty
4	547	0.71	0.80	68	empty
5	551	0.71	0.80	49	empty

Interfaces

7 interfaces between chains.

8–1 · 4749 Å² buried · 47 hydrogen bonds · protein-protein
5–8 · 4421 Å² buried · 35 hydrogen bonds · protein-protein
5–4 · 3223 Å² buried · 36 hydrogen bonds · protein-protein
5–1 · 2422 Å² buried · 17 hydrogen bonds · protein-protein
8–9 · 1372 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6SWY · Structure of active GID E3 ubiquitin ligase complex minus Gid2 and delta Gid9 RING domain · the same entry in another collection · chain 9 against 9, TM-score 1.00
P40547 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 28 (P40547) · a predicted model of the same protein · chain 5 against A, TM-score 1.00
P38263 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 24 (P38263) · a predicted model of the same protein · chain 4 against A, TM-score 0.87
P40208 · AlphaFold monomer V2.0 prediction for glucose-induced degradation protein 8 (P40208) · a predicted model of the same protein · chain 8 against A, TM-score 0.69
P40492 · AlphaFold monomer V2.0 prediction for protein FYV10 (P40492) · a predicted model of the same protein · chain 9 against A, TM-score 0.65
P53076 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 30 (P53076) · a predicted model of the same protein · chain 1 against A, TM-score 0.57

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 P40547
Every structure of UniProt P40208
Every structure of UniProt P53076
Every structure of UniProt P38263
Every structure of UniProt P40492
Elsewhere: RCSB PDB 6SWY · PDBe 6SWY · UniProt P40547 · UniProt P40208 · UniProt P53076 · UniProt P38263 · UniProt P40492

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