MolNFT v1 · #158554 · protein

Ubiquitin binding variants

6NXL · Polyubiquitin-B: “Ubiquitin binding variants”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #158554 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NXL
Type: protein
Length: 592 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-B
UniProt: B4DV12
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Polyubiquitin-B	protein	75	24% helix, 45% strand	B4DV12
B, D, F	Polyubiquitin-B	protein	74	24% helix, 43% strand	B4DV12
C, G	Polyubiquitin-B	protein	73	25% helix, 42% strand	B4DV12
H	Polyubiquitin-B	protein	74	24% helix, 43% strand	B4DV12

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.74	0.83	60	empty
2	233	0.66	0.83	40	empty
3	51	0.37	0.81	16	empty
4	52	0.37	0.80	16	empty
5	50	0.32	0.78	15	empty

Interfaces

20 interfaces between chains.

G–H · 1722 Å² buried · 42 hydrogen bonds · protein-protein
A–E · 1702 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 1701 Å² buried · 40 hydrogen bonds · protein-protein
B–F · 1695 Å² buried · 41 hydrogen bonds · protein-protein
D–F · 696 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6NXL · Ubiquitin binding variants · the same entry in another collection · chain A against A, TM-score 1.00

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 B4DV12
Elsewhere: RCSB PDB 6NXL · PDBe 6NXL · UniProt B4DV12

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