MolNFT v1 · #113430 · protein

Structure of LYS33-linked diub bound to trabid NZF1

5AF6 · Ubiquitin: “Structure of LYS33-linked diub bound to trabid NZF1”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.81). MolNFT v1 #113430 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AF6
Type: protein
Length: 520 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; Trabid
UniProt: Q96C32, Q9UGI0
Ligands: ZN
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Ubiquitin	protein	76	16% helix, 33% strand	Q96C32
F, J	Trabid	protein	28	0% helix, 21% strand	Q9UGI0
G	Trabid	protein	29	0% helix, 21% strand	Q9UGI0
H	Trabid	protein	28	0% helix, 21% strand	Q9UGI0
I	Trabid	protein	27	0% helix, 22% strand	Q9UGI0

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains F, G, H, I, J

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

Pockets

5 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	1023	0.81	0.82	132	empty
2	80	0.36	0.76	22	empty
3	50	0.32	0.77	12	empty
4	54	0.28	0.75	16	empty
5	50	0.28	0.75	12	empty

Interfaces

16 interfaces between chains.

A–H · 473 Å² buried · 4 hydrogen bonds · protein-protein
E–J · 446 Å² buried · 6 hydrogen bonds · protein-protein
C–J · 438 Å² buried · 3 hydrogen bonds · protein-protein
C–E · 434 Å² buried · 11 hydrogen bonds · protein-protein
B–I · 430 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 isopeptide (isopeptide).

Compared structures

5AF6 · Structure of Lys33-linked diUb bound to Trabid NZF1 · the same entry in another collection · chain J against J, TM-score 1.00
Q9UGI0 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase ZRANB1 (Q9UGI0) · a predicted model of the same protein · chain I 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 Q96C32
Every structure of UniProt Q9UGI0
Elsewhere: RCSB PDB 5AF6 · PDBe 5AF6 · UniProt Q96C32 · UniProt Q9UGI0

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