SMTL ID : 6z1v.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 7 residues within 4Å: Chain A: E.9, E.12, F.13, D.16, T.17, K.20, Q.28 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.9, A:D.16, A:T.17, A:K.20, A:Q.28

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: S.53, D.54, K.58, L.62 Chain B: T.52, W.53, S.54, D.56, I.57 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.58, B:T.52, B:T.52

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 6 residues within 4Å: Chain B: G.9, R.10, L.11, Q.118, V.119, T.120 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.118 Hydrogen bonds: B:T.120 Water bridges: B:G.9, B:Q.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oosterheert, W. et al., Implications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F. Life Sci Alliance (2020)

Release Date

2020-09-23

Peptides

CD9 antigen: A
Nanobody 4E8: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CD9 antigen

Nanobody 4E8

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