MolNFT v1 · #37761 · protein

Crystal structure of the 35-36 moad insertion mutant of ubiquitin

2GBR: “Crystal structure of the 35-36 moad insertion mutant of ubiquitin”. X-ray diffraction, 1 ligand (CD), 3 pockets (best druggability 0.51). MolNFT v1 #37761 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GBR
Type: protein
Length: 230 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P62988
Ligands: CD
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ubiquitin	protein	77	29% helix, 32% strand	P62988
C	Ubiquitin	protein	76	24% helix, 30% strand	P62988

Ligands and binding sites

CD · Cadmium ion · metal · 13 copies · chains A, B, C

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

Pockets

3 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	89	0.51	0.83	22	CD
2	96	0.38	0.75	17	empty
3	99	0.35	0.74	16	empty

Interfaces

2 interfaces between chains.

A–B · 349 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 211 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2GBR · Crystal Structure of the 35-36 MoaD 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 2GBR · PDBe 2GBR · UniProt P62988

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