SMTL ID : 8rp8.1 (1 other biounit)

Structure of K2 Fab in complex with human CD47 ECD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PEG.1: 6 residues within 4Å: Chain A: S.99, A.102, D.104 Chain B: Y.49, Q.55 Chain C: T.102 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:Y.49, B:Q.55, A:A.102 Hydrogen bonds: A:S.99, A:S.99, A:D.104

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: G.42, K.43, G.44 Chain B: T.85, Y.87, Q.101, G.102 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.87, B:G.102, A:G.42 Water bridges: B:T.85, B:T.85, B:K.104, A:Q.39, A:G.44

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

NAG.3: 7 residues within 4Å: Chain C: E.11, F.12, N.16, T.18, V.19, V.20, L.111 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.12, C:V.19, C:L.111 Hydrogen bonds: C:E.11, C:N.16, C:V.20 Water bridges: C:T.13 NAG.4: 1 residues within 4Å: Chain C: N.55 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain C: G.92, N.93, E.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.93, C:E.110 Water bridges: C:N.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malinge, P. et al., Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1. Mabs (2024)

Release Date

2024-06-19

Peptides

K2 Fab heavy chain: A
K2 Fab light chain: B
Leukocyte surface antigen CD47: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

K2 Fab heavy chain

K2 Fab light chain

Leukocyte surface antigen CD47

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