SMTL ID : 7kx0.1

Crystal structure of the CD27:CD70 co-stimulatory complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG-BMA-FUC.1: 4 residues within 4Å: Chain A: N.28, H.29, W.40, G.59 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.29 NAG-NAG-BMA-FUC.3: 4 residues within 4Å: Chain B: N.28, H.29, W.40, G.59 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.29

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.2: 6 residues within 4Å: Chain A: D.35, P.36, R.37, C.98, N.135 Chain E: K.93 No protein-ligand interaction detected (PLIP)

2 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.4: 7 residues within 4Å: Chain B: D.35, P.36, R.37, C.98, S.106, N.135 Chain F: K.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 5 residues within 4Å: Chain C: P.36, R.37, C.98, N.135 Chain D: K.93 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-FUC.5: 4 residues within 4Å: Chain C: N.28, H.29, W.40, G.59 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 12 residues within 4Å: Chain A: L.110, T.117, I.118, A.119 Chain B: L.110, T.117, I.118, A.119 Chain C: L.110, T.117, I.118, A.119 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:A.119, C:A.119, B:A.119, B:A.119 Water bridges: B:T.117

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

NAG.8: 3 residues within 4Å: Chain D: L.70, V.71, N.73 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.73 NAG.9: 3 residues within 4Å: Chain E: L.70, V.71, N.73 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.73 NAG.10: 3 residues within 4Å: Chain F: L.70, V.71, N.73 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Structural delineation and phase-dependent activation of the costimulatory CD27:CD70 complex. J.Biol.Chem. (2021)

Release Date

2021-09-08

Peptides

CD70 antigen: ABC
CD27 antigen: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

CD70 antigen

CD27 antigen