MolNFT v1 · #56349 · protein

Crystal structure of ubiquitin P37A/P38A

2ZCB: “Crystal structure of ubiquitin P37A/P38A”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.54). MolNFT v1 #56349 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ZCB
Type: protein
Length: 219 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P62988
Ligands: ZN
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin	protein	74	24% helix, 34% strand	P62988
B	Ubiquitin	protein	73	25% helix, 34% strand	P62988
C	Ubiquitin	protein	72	25% helix, 29% strand	P62988

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, C, B

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

Pockets

3 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	111	0.54	0.83	23	empty
2	67	0.53	0.86	23	empty
3	50	0.36	0.80	11	empty

Interfaces

3 interfaces between chains.

A–C · 380 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 377 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 251 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2ZCB · Crystal Structure of ubiquitin P37A/P38A · 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 2ZCB · PDBe 2ZCB · UniProt P62988

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