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

Crystal structure of human CD47 ECD bound to Fab of Hu1C8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.93, Y.94, D.97 Chain B: D.101 Chain C: K.41 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.101, A:D.93, A:Y.94, H2O.3, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain B: A.119, S.120, F.151, G.179, L.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.120, B:G.179

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

NAG.3: 4 residues within 4Å: Chain B: I.53 Chain C: N.93, I.108, E.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.93, C:E.110 Water bridges: C:N.93 NAG.4: 7 residues within 4Å: Chain C: V.10, E.11, F.12, N.16, T.18, V.19, V.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.10 Hydrogen bonds: C:E.11, C:N.16, C:V.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, X. et al., The humanized antibody Hu1C8 binds to a distinct epitope of CD47 in a novel metal ion-dependent manner to induce low RBC toxicity and effective antitumour activity. To Be Published

Release Date

2025-05-07

Peptides

1C8 Fab light chain: A
1C8 Fab heavy chain: B
Leukocyte surface antigen CD47: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
F

1C8 Fab light chain

1C8 Fab heavy chain

Leukocyte surface antigen CD47

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