MolNFT v1 · #46521 · protein

Crystal structure and solution NMR studies of LYS48-linked tetraubiquitin at neutral pH

2O6V: “Crystal structure and solution NMR studies of LYS48-linked tetraubiquitin at neutral pH”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.83). MolNFT v1 #46521 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2O6V
Type: protein
Length: 605 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P62988
Ligands: SO4
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 22% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Ubiquitin	protein	75	24% helix, 33% strand	P62988
B, F	Ubiquitin	protein	76	20% helix, 34% strand	P62988
C, G	Ubiquitin	protein	76	25% helix, 34% strand	P62988
D	Ubiquitin	protein	76	24% helix, 34% strand	P62988
H	Ubiquitin	protein	75	16% helix, 32% strand	P62988

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E, F
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, D

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.83	0.96	38	empty
2	203	0.83	0.96	39	empty
3	115	0.59	0.86	25	empty
4	126	0.41	0.75	20	empty
5	65	0.34	0.76	17	empty

Interfaces

14 interfaces between chains.

C–D · 775 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 755 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 698 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 671 Å² buried · 10 hydrogen bonds · protein-protein
E–G · 313 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 isopeptide, 2 modified (isopeptide, nonstandard).

Compared structures

2O6V · Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH · 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 P62988
Elsewhere: RCSB PDB 2O6V · PDBe 2O6V · UniProt P62988

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