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Crystal structure of E3 ligase in complex with peptide

Analyse Crystal structure of E3 ligase in complex with peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JYA
Type: protein
Length: 1,133 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein fem-1 homolog C; Asn-arg-arg-arg-arg-TRP-arg-glu-arg-gln-arg
UniProt: Q96JP0
Ligands: UNX
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein fem-1 homolog C	protein	370	59% helix, 4% strand	Q96JP0
C	Protein fem-1 homolog C	protein	369	56% helix, 4% strand	Q96JP0
D	Asn-arg-arg-arg-arg-TRP-arg-glu-arg-gln-arg	protein	10	0% helix, 0% strand	—
E	Asn-arg-arg-arg-arg-TRP-arg-glu-arg-gln-arg	protein	8	0% helix, 0% strand	—
F	Asn-arg-arg-arg-arg-TRP-arg-glu-arg-gln-arg	protein	6	0% helix, 0% strand	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 5 copies · chains A, C, B

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.78	0.80	85	empty
2	1018	0.73	0.76	92	empty
3	484	0.73	0.82	61	empty
4	58	0.64	0.94	18	empty
5	352	0.58	0.76	31	empty

Interfaces

9 interfaces between chains.

A–B · 893 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 861 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 857 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 825 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 728 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7JYA · Crystal structure of E3 ligase in complex with peptide · the same entry in another collection · chain F against F, TM-score 1.00
Q96JP0 · AlphaFold monomer V2.0 prediction for protein fem-1 homolog C (Q96JP0) · a predicted model of the same protein · chain B 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 Q96JP0
Elsewhere: RCSB PDB 7JYA · PDBe 7JYA · UniProt Q96JP0

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