SMTL ID : 8byu.1

Crystal Structure of HexaBody-CD38 Fab in complex with CD38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: P.14, R.87, S.88, E.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.87, A:S.88, A:S.88 Water bridges: A:G.15 SO4.4: 6 residues within 4Å: Chain C: W.87, S.88, R.89, S.182, T.183, F.184 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.89, C:T.183, C:T.183, C:F.184 Water bridges: C:W.87 Salt bridges: C:R.89 SO4.5: 2 residues within 4Å: Chain C: R.174, S.175 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.175 Water bridges: C:K.176 Salt bridges: C:R.174

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: G.8, A.9, E.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.7, A:E.10 GOL.3: 11 residues within 4Å: Chain A: F.174, P.175, V.177, S.185, L.186, S.187 Chain B: Q.160, S.162, S.176, S.177, T.178 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:F.174, A:S.185, A:S.187, B:Q.160, B:S.162 Water bridges: B:T.178, B:T.178

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

EDO.6: 4 residues within 4Å: Chain C: W.87, K.91, E.108, W.151 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.108, C:E.108 Water bridges: C:K.91 EDO.7: 7 residues within 4Å: Chain A: R.103 Chain B: R.30, W.32, N.92 Chain C: D.164, V.165, Q.198 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:N.92, C:Q.198, A:R.103 Water bridges: C:V.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiemstra, I.H. et al., Preclinical anti-tumour activity of HexaBody-CD38, a next-generation CD38 antibody with superior complement-dependent cytotoxic activity. Ebiomedicine (2023)

Release Date

2023-07-12

Peptides

Fab Heavy Chain: A
Fab Light Chain: B
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

Fab Heavy Chain

Fab Light Chain

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1