MolNFT v1 · #158553 · protein

Ubiquitin binding variants

6NXK · Polyubiquitin-C: “Ubiquitin binding variants”. X-ray diffraction, 3 pockets (best druggability 0.51). MolNFT v1 #158553 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NXK
Type: protein
Length: 296 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-C; Anaphase-promoting complex subunit 2
UniProt: P0CG48, Q9UJX6
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Polyubiquitin-C	protein	73	25% helix, 34% strand	P0CG48
C	Anaphase-promoting complex subunit 2	protein	76	62% helix, 9% strand	Q9UJX6
D	Anaphase-promoting complex subunit 2	protein	74	66% helix, 11% strand	Q9UJX6

Pockets

3 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	175	0.51	0.77	27	empty
2	104	0.44	0.78	16	empty
3	55	0.32	0.76	10	empty

Interfaces

5 interfaces between chains.

A–C · 485 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 436 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 383 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 366 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 288 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6NXK · Ubiquitin binding variants · the same entry in another collection · chain A against A, TM-score 1.00
Q9UJX6 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 2 (Q9UJX6) · a predicted model of the same protein · chain D against A, TM-score 0.86

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 P0CG48
Every structure of UniProt Q9UJX6
Elsewhere: RCSB PDB 6NXK · PDBe 6NXK · UniProt P0CG48 · UniProt Q9UJX6

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