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Crystal structure of protac MS33 in complex with the wd repeat- containing protein 5 and PVHL:ELONGINC:ELONGINB

Analyse Crystal structure of protac MS33 in complex with the wd repeat- containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JTO
Type: protein
Length: 641 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Wd repeat-containing protein 5; Elongin-B; Elongin-C; Von hippel-lindau disease tumor…
UniProt: P61964, Q15370, Q15369, P40337
Ligands: VKA, NA, SCN
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Wd repeat-containing protein 5	protein	303	0% helix, 52% strand	P61964
J	Elongin-B	protein	103	18% helix, 39% strand	Q15370
K	Elongin-C	protein	87	48% helix, 15% strand	Q15369
L	Von hippel-lindau disease tumor suppressor	protein	148	25% helix, 30% strand	P40337

Ligands and binding sites

VKA · 3-methyl-N-(11-{[2-(4-{[4'-(4-methylpiperazin-1-yl)-3'-{[6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carbonyl]amino}[1,1'-biphenyl]-3-yl]methyl}piperazin-1-yl)ethyl]amino}-11-oxoundecanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl) phenyl]methyl}-L-prolinamide · ligand · chains B, L
NA · Sodium ion · metal · chains L
SCN · Thiocyanate ion · ion · 4 copies · chains B, J
EDO · 1,2-ethanediol · additive · 5 copies · chains B, K, L
GOL · Glycerol · additive · chains K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.75	0.81	67	empty
2	165	0.44	0.75	23	empty
3	130	0.39	0.74	17	empty
4	71	0.34	0.75	16	EDO

Interfaces

4 interfaces between chains.

J–K · 1120 Å² buried · 14 hydrogen bonds · protein-protein
K–L · 1059 Å² buried · 13 hydrogen bonds · protein-protein
J–L · 188 Å² buried · 0 hydrogen bonds · protein-protein
B–L · 159 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7JTO · Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and… · the same entry in another collection · chain B against B, TM-score 1.00
Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain J against A, TM-score 0.98
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain K against A, TM-score 0.98

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 P61964
Every structure of UniProt Q15370
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Every structure of UniProt P40337
Elsewhere: RCSB PDB 7JTO · PDBe 7JTO · UniProt P61964 · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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