SMTL ID : 5tzu.1

Crystal structure of human CD47 ECD bound to Fab of B6H12.2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain C: E.11, F.12, N.16, T.18, V.19, V.20, L.111 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 8 residues within 4Å: Chain B: T.28, G.31, Y.32 Chain C: N.32, T.34 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3, ACT.6 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 6 residues within 4Å: Chain C: T.33, T.34, G.52, N.55 Ligands: NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: T.28, G.68, S.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.69 Water bridges: A:S.67, A:S.67, A:D.70 SO4.5: 2 residues within 4Å: Chain B: A.119, S.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.120, B:S.120

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

ACT.6: 5 residues within 4Å: Chain B: F.27, T.28, Y.32 Ligands: NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:Y.32 Water bridges: B:Y.32 ACT.7: 3 residues within 4Å: Chain B: S.7, G.8, G.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.8, B:G.9 Water bridges: B:T.112 ACT.11: 3 residues within 4Å: Chain C: T.7, K.8, S.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.7 Hydrogen bonds: C:K.8, C:S.9, C:S.9

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

NAG.8: 5 residues within 4Å: Chain C: N.5, F.24, V.25, T.26, K.75 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.5 NAG.9: 2 residues within 4Å: Chain C: N.93, E.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.110 Water bridges: C:N.93

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain C: D.83, K.84, S.85 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.17, C:K.84, C:S.85, C:S.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pietsch, E.C. et al., Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies. Blood Cancer J (2017)

Release Date

2017-03-15

Peptides

Light Chain of Fab B6H12.2: A
Heavy Chain of Fab B6H12.2: B
Leukocyte surface antigen CD47: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
C

Light Chain of Fab B6H12.2

Heavy Chain of Fab B6H12.2

Leukocyte surface antigen CD47

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