SMTL ID : 9gox.1

Crystal structure of Fab B6-D9 in complex with CD38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: V.93, Q.113, G.114, T.115, L.116 Chain B: G.41 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.116 SO4.8: 7 residues within 4Å: Chain C: W.81, S.82, R.83, S.176, T.177 Ligands: GOL.11, EPE.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.83, C:T.177 Water bridges: C:F.178 Salt bridges: C:R.83

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

EDO.2: 6 residues within 4Å: Chain A: R.38, Q.39, A.40, Q.43, G.44, E.46 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.38, A:A.40, A:G.44, A:E.46 Water bridges: A:G.44 EDO.3: 6 residues within 4Å: Chain A: G.42, Q.43 Chain B: V.85, Y.87, Q.100, G.101 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.43, B:Y.87 EDO.4: 3 residues within 4Å: Chain B: K.39, Q.42, R.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.39 Water bridges: B:Q.42 EDO.9: 5 residues within 4Å: Chain C: T.58, E.59, V.143, K.146 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.146 Water bridges: C:T.58, C:E.59, C:E.59, C:E.59 EDO.10: 4 residues within 4Å: Chain C: C.55, N.56, T.58 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: H.31, Y.102 Chain C: N.226, Q.228 Ligands: EDO.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.31 Water bridges: C:N.226, C:Q.228 EDO.13: 2 residues within 4Å: Chain C: Q.228 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.228 EDO.15: 4 residues within 4Å: Chain C: T.92, R.96, M.98, F.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.92 Water bridges: C:H.30 EDO.16: 4 residues within 4Å: Chain C: E.102, D.103, Y.108, D.111 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Q.93, C:Q.93, C:D.103

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 6 residues within 4Å: Chain C: R.83, I.84, N.165, S.167, R.168, G.201 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.84 Water bridges: C:R.83, C:I.84 NAG.6: 3 residues within 4Å: Chain C: W.132, K.174, N.175 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.132 Hydrogen bonds: C:N.175 NAG.7: 3 residues within 4Å: Chain C: K.52, N.56, T.58 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.52 Water bridges: C:K.52, C:N.56, C:D.61

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain C: W.81, L.101, E.102, W.145, T.177 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.177 Water bridges: C:W.145, C:F.178

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 3 residues within 4Å: Chain C: R.150, V.181, N.185 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.185 Salt bridges: C:R.150

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.17: 9 residues within 4Å: Chain C: R.83, W.132, S.142, W.145, K.146, N.175, T.177, S.180 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.180 Salt bridges: C:R.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loyau, J. et al., Biparatopic binding of ISB 1442 to CD38 in trans enables increased cell antibody density and increased avidity. Mabs (2025)

Release Date

2025-02-12

Peptides

Fab B6-D9 heavy chain: A
Fab B6-D9 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 B6-D9 heavy chain

Fab B6-D9 light chain

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1

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