SMTL ID : 6y8k.1

Crystal structure of CD137 in complex with the cyclic peptide BCY10916

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: Q.125, K.126, R.127 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.126 Hydrogen bonds: A:Q.125, A:K.126 Salt bridges: A:R.127

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

EDO.2: 11 residues within 4Å: Chain A: C.103, K.104, Q.105, Q.107, E.108, L.109, N.123, Q.125, K.126, R.127, G.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.104, A:L.109, A:K.126 Water bridges: A:C.103, A:G.128

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

SO4.3: 5 residues within 4Å: Chain A: D.84, C.85, H.90, C.91, R.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.91 Salt bridges: A:R.127 SO4.4: 1 residues within 4Å: Chain A: R.151 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.151 SO4.5: 3 residues within 4Å: Chain A: T.148, K.149, E.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.149

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: S.52, S.79, N.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.52, A:S.52, A:N.80

1 x 29N: 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one(Covalent)

29N.7: 12 residues within 4Å: Chain A: L.92, S.97, M.98 Chain B: C.1, I.2, E.3, E.4, G.5, C.8, F.9, A.10, C.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Upadhyaya, P. et al., Anticancer immunity induced by a synthetic tumor-targeted CD137 agonist. J Immunother Cancer (2021)

Release Date

2021-02-03

Peptides

Tumor necrosis factor receptor superfamily member 9: A
BCY10916: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
PPP

Tumor necrosis factor receptor superfamily member 9

BCY10916