SMTL ID : 8zye.1

Crystal structure of CD38 in complex with RP02 antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: W.81, S.82, R.83, S.176, T.177, F.178 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.81, A:R.83, A:R.83, A:T.177, A:F.178

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

SO4.2: 3 residues within 4Å: Chain A: C.136, S.137, N.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.137, A:N.138 SO4.3: 2 residues within 4Å: Chain A: R.168, S.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.169 Salt bridges: A:R.168 SO4.8: 8 residues within 4Å: Chain A: R.96, D.97 Chain B: G.146, N.147, N.148, Y.149, N.168, K.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.147, B:N.168 Salt bridges: B:K.183

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

EDO.4: 8 residues within 4Å: Chain A: L.79, L.80, W.81, T.100, L.101, F.152, E.182 Ligands: PEG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.81, A:L.101, A:E.182 EDO.5: 1 residues within 4Å: Chain A: R.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.236 EDO.6: 2 residues within 4Å: Chain A: Q.39, W.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.39 EDO.7: 5 residues within 4Å: Chain A: G.69, Q.71, T.104, V.148, R.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.71, A:R.151 EDO.9: 6 residues within 4Å: Chain B: L.46, E.47, W.48, S.118, V.119, F.217 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.48, B:W.48, B:S.118, B:V.119, B:F.217 EDO.10: 3 residues within 4Å: Chain B: H.54, S.55, K.74 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.54, B:K.74, B:K.74 EDO.11: 6 residues within 4Å: Chain B: D.202, Y.204, G.219, G.220, T.221, K.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, Y., CD38 CAR antigen engagement mechanisms and affinity tuning. To Be Published

Release Date

2025-09-17

Peptides

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1: A
RP02 scFv: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1

RP02 scFv