MolNFT v1 · #110038 · protein

Crystal structure of the airapl tandem uims in complex with a LYS48- linked tri-ubiquitin

4XKH · Polyubiquitin-C: “Crystal structure of the airapl tandem uims in complex with a LYS48- linked tri-ubiquitin”. X-ray diffraction, 6 pockets (best druggability 0.54). MolNFT v1 #110038 on GenesisL1: 3D structure, binding sites and…

PDB: 4XKH
Type: protein
Length: 564 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-C; AN1-type zinc finger protein 2B
UniProt: P0CH28, Q91X58
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 6 distinct chains · 29% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyubiquitin-C	protein	72	19% helix, 24% strand	P0CH28
E	AN1-type zinc finger protein 2B	protein	43	60% helix, 0% strand	Q91X58
F, D, I	Polyubiquitin-C	protein	73	21% helix, 33% strand	P0CH28
B	Polyubiquitin-C	protein	74	23% helix, 28% strand	P0CH28
C, H	AN1-type zinc finger protein 2B	protein	40	65% helix, 0% strand	Q91X58
G	Polyubiquitin-C	protein	76	14% helix, 33% strand	P0CH28

Pockets

6 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	59	0.54	0.88	19	empty
2	64	0.47	0.83	15	empty
3	62	0.46	0.83	16	empty
4	104	0.39	0.76	19	empty
5	87	0.34	0.75	20	empty

Interfaces

11 interfaces between chains.

A–E · 788 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 748 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 725 Å² buried · 5 hydrogen bonds · protein-protein
F–B · 410 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 347 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4XKH · Crystal structure of the airapl tandem uims in complex with a LYS48-linked tri-ubiquitin · the same entry in another collection · chain I against I, TM-score 1.00
P0CH28 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CH28) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 P0CH28
Every structure of UniProt Q91X58
Elsewhere: RCSB PDB 4XKH · PDBe 4XKH · UniProt P0CH28 · UniProt Q91X58

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