SMTL ID : 5iwl.1

CD47-diabody complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain C: D.11, F.12, N.16, V.19, V.20 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.12, C:V.19 Hydrogen bonds: C:D.11, C:N.16, C:V.20 NAG.2: 1 residues within 4Å: Chain C: N.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:T.34 NAG.3: 2 residues within 4Å: Chain C: N.93, E.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.93, C:E.110 NAG.5: 2 residues within 4Å: Chain D: N.32, T.34 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain D: D.11, F.12, N.16, V.19, V.20 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.12, D:V.19 Hydrogen bonds: D:D.11, D:N.16, D:V.20 NAG.7: 3 residues within 4Å: Chain D: G.92, N.93, E.110 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.93, D:E.110

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 9 residues within 4Å: Chain A: Y.101, R.102 Chain B: N.155, Y.159 Chain C: L.2, E.97, E.104, G.105, E.106 7 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:R.102, A:R.102, C:E.104, C:G.105, C:E.106, B:N.155, B:Y.159 PGE.8: 8 residues within 4Å: Chain A: N.155, Y.159 Chain B: Y.101, R.102 Chain D: E.97, E.104, G.105, E.106 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:E.104, D:E.106, D:E.106, A:N.155, B:R.102, B:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weiskopf, K. et al., CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer. J.Clin.Invest. (2016)

Release Date

2016-06-29

Peptides

5F9 diabody: AB
Leukocyte surface antigen CD47: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

5F9 diabody

Leukocyte surface antigen CD47