SMTL ID : 7d4b.1

Crystal structure of 4-1BB in complex with a VHH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN-FUC.1: 2 residues within 4Å: Chain A: N.114, L.117 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: F.98, N.125 Chain B: N.59, D.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.62

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: K.45, G.46 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: C.70, R.106 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: R.19, K.76 Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: E.87, C.97, I.108 No protein-ligand interaction detected (PLIP) SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.10: 2 residues within 4Å: Chain B: W.106, M.108 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain B: T.28, R.72, N.74, N.77, T.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.28, B:T.78 EDO.9: 1 residues within 4Å: Chain B: K.65 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhai, T. et al., Generation of a safe and efficacious llama single-domain antibody fragment (vHH) targeting the membrane-proximal region of 4-1BB for engineering therapeutic bispecific antibodies for cancer. J Immunother Cancer (2021)

Release Date

2021-07-14

Peptides

Tumor necrosis factor receptor superfamily member 9: A
anti-4-1BB VHH: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tumor necrosis factor receptor superfamily member 9

anti-4-1BB VHH