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Structure of the EC2 domain of CD9 in complex with nanobody 4C8

Analyse Structure of the EC2 domain of CD9 in complex with nanobody 4C8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z20
Type: protein
Length: 398 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD9 antigen; Nanobody 4C8
UniProt: P21926
Ligands: CL

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD9 antigen	protein	79	63% helix, 5% strand	P21926
B, D	Nanobody 4C8	protein	120	8% helix, 51% strand	—
C	CD9 antigen	protein	79	65% helix, 3% strand	P21926

Ligands and binding sites

CL · Chloride ion · ion · chains D
GOL · Glycerol · additive · 2 copies · chains B, D

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

Interfaces

3 interfaces between chains.

A–C · 713 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 675 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 605 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6Z20 · Structure of the EC2 domain of CD9 in complex with nanobody 4C8 · 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 0.71

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 6Z20 · PDBe 6Z20 · UniProt P21926

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