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GUMBY/FAM105B in complex with linear di-ubiquitin

Analyse GUMBY/FAM105B in complex with linear di-ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KSL
Type: protein
Length: 4,951 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein FAM105B; Polyubiquitin-C
UniProt: Q96BN8, P0CG48
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 9 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein FAM105B	protein	263	55% helix, 11% strand	Q96BN8
D, H, P, T, X	Polyubiquitin-C	protein	149	22% helix, 33% strand	P0CG48
C, F, J, L, N, R, V	Polyubiquitin-C	protein	150	22% helix, 34% strand	P0CG48
E, I	Protein FAM105B	protein	262	56% helix, 11% strand	Q96BN8
G, Q, U	Protein FAM105B	protein	261	56% helix, 11% strand	Q96BN8
K, O	Protein FAM105B	protein	270	55% helix, 11% strand	Q96BN8
M	Protein FAM105B	protein	260	54% helix, 11% strand	Q96BN8
S	Protein FAM105B	protein	263	55% helix, 11% strand	Q96BN8
W	Protein FAM105B	protein	260	56% helix, 12% strand	Q96BN8

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	901	0.78	0.80	99	empty
2	955	0.77	0.79	97	empty
3	710	0.76	0.81	77	empty
4	983	0.76	0.78	102	empty
5	161	0.75	0.92	27	empty

Interfaces

52 interfaces between chains.

B–C · 1898 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 1890 Å² buried · 30 hydrogen bonds · protein-protein
U–V · 1890 Å² buried · 29 hydrogen bonds · protein-protein
O–P · 1876 Å² buried · 32 hydrogen bonds · protein-protein
I–J · 1869 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

4KSL · Gumby/Fam105B in complex with linear di-ubiquitin · the same entry in another collection · chain I against I, 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 Q96BN8
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 4KSL · PDBe 4KSL · UniProt Q96BN8 · UniProt P0CG48

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