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Crystal structure of the 35-36 8 glycine insertion mutant of ubiquitin

Analyse Crystal structure of the 35-36 8 glycine insertion mutant of ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GBM
Type: protein
Length: 321 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P62988
Ligands: ARS
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin	protein	81	21% helix, 31% strand	P62988
B, C, D	Ubiquitin	protein	80	25% helix, 31% strand	P62988

Ligands and binding sites

ARS · Arsenic · metal · 3 copies · chains B, C, D

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

Pockets

4 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	441	0.67	0.79	49	empty
2	83	0.51	0.83	20	empty
3	74	0.35	0.76	20	empty
4	95	0.34	0.74	16	empty

Interfaces

4 interfaces between chains.

A–B · 363 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 355 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 257 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 257 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2GBM · Crystal Structure of the 35-36 8 Glycine Insertion Mutant of Ubiquitin · 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 2GBM · PDBe 2GBM · UniProt P62988

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