SMTL ID : 8rp8.2 (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

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

NAG.1: 8 residues within 4Å: Chain A: V.10, E.11, F.12, N.16, T.18, V.19, V.20, L.111 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.10, A:F.12, A:V.19, A:L.111 Hydrogen bonds: A:E.11, A:N.16, A:V.20 Water bridges: A:E.11, A:T.13 NAG.2: 1 residues within 4Å: Chain A: N.55 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: G.92, N.93, E.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.93, A:E.110 Water bridges: A:N.93

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

PEG.4: 6 residues within 4Å: Chain A: T.102 Chain B: S.99, A.102, D.104 Chain C: Y.49, Q.55 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.99, B:S.99 Water bridges: B:K.98, B:A.102, A:T.102

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: G.42, K.43, G.44 Chain C: T.85, Y.87, Q.101, G.102 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.101, C:G.102, B:G.42 Water bridges: C:K.104, B:Q.39, B:G.44

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

C
L

Leukocyte surface antigen CD47

K2 Fab heavy chain

K2 Fab light chain

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