MolNFT v1 · #182991 · protein

Branched LYS48- and LYS63-linked tri-ubiquitin (K48-K63-UB3) in complex with synthetic nanobody NBSL3

7NBB · Polyubiquitin-B: “Branched LYS48- and LYS63-linked tri-ubiquitin (K48-K63-UB3) in complex with synthetic nanobody NBSL3”. X-ray diffraction, 3 ligands (MG, NA, CL), 7 pockets (best druggability 0.74). MolNFT v1 #182991 on GenesisL1…

PDB: 7NBB
Type: protein
Length: 683 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyubiquitin-B; Synthetic nanobody NBSL3
UniProt: J3QS39
Ligands: MG, NA, CL
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Polyubiquitin-B	protein	71	25% helix, 32% strand	J3QS39
B, C, F, G	Polyubiquitin-B	protein	76	24% helix, 33% strand	J3QS39
D	Synthetic nanobody NBSL3	protein	119	6% helix, 55% strand	—
H	Synthetic nanobody NBSL3	protein	118	6% helix, 57% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, H, F, G
NA · Sodium ion · metal · 2 copies · chains C, F, G, H
CL · Chloride ion · ion · 7 copies · chains C, D, E, F, G, H
GOL · Glycerol · additive · 2 copies · chains B, C, F, G

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

Pockets

7 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	939	0.74	0.78	83	CL
2	167	0.49	0.78	29	GOL, MG
3	154	0.49	0.78	31	GOL, MG, CL
4	66	0.38	0.78	17	empty
5	71	0.38	0.78	17	empty

Interfaces

17 interfaces between chains.

C–D · 913 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 893 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 547 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 542 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 465 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 isopeptide, 1 disulfide (isopeptide, disulfide).

Compared structures

7NBB · Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic… · 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 J3QS39
Elsewhere: RCSB PDB 7NBB · PDBe 7NBB · UniProt J3QS39

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