Research workbench

Structure of the EC2 domain of CD9 in complex with nanobody 4E8

Analyse Structure of the EC2 domain of CD9 in complex with nanobody 4E8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z1V
Type: protein
Length: 203 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD9 antigen; Nanobody 4E8
UniProt: P21926

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD9 antigen	protein	80	64% helix, 4% strand	P21926
B	Nanobody 4E8	protein	123	7% helix, 48% strand	—

Ligands and binding sites

PGE · Triethylene glycol · additive · chains A
EDO · 1,2-ethanediol · additive · chains A, B
ACY · Acetic acid · additive · chains B

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

Interfaces

1 interface between chains.

A–B · 680 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6Z1V · Structure of the EC2 domain of CD9 in complex with nanobody 4E8 · the same entry in another collection · chain A against A, TM-score 1.00
P21926 · AlphaFold monomer V2.0 prediction for CD9 antigen (P21926) · a predicted model of the same protein · chain A against A, TM-score 0.72

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 P21926
Elsewhere: RCSB PDB 6Z1V · PDBe 6Z1V · UniProt P21926

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.