SMTL ID : 6mi2.2 (1 other biounit)

Structure of the human 4-1BB / Utomilumab Fab complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain C: V.122, L.123, V.124, N.125 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.122 Hydrogen bonds: C:N.125

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

SO4.2: 5 residues within 4Å: Chain A: E.1, V.2, Y.105 Chain C: A.73, G.74 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.1, A:E.1, A:E.1, A:V.2, A:Y.105, A:Y.105, C:G.74 SO4.3: 3 residues within 4Å: Chain A: K.87, A.88, S.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.88, A:S.89 SO4.4: 8 residues within 4Å: Chain B: E.82, V.107, G.109, Q.110, Y.142, K.168, N.172, Y.174 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.82, B:G.109, B:Q.110, B:Y.142, B:N.172 Salt bridges: B:K.168 SO4.5: 3 residues within 4Å: Chain B: S.66, N.68, T.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.68, B:N.68 SO4.8: 1 residues within 4Å: Chain C: K.105 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.105 SO4.9: 2 residues within 4Å: Chain C: R.49, P.66 2 PLIP interactions: 2 interactions with chain C Water bridges: C:G.67 Salt bridges: C:R.49

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain B: K.168, Y.174 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.168, B:K.168, B:K.168, B:Y.174 GOL.7: 3 residues within 4Å: Chain B: S.55, G.56 Chain C: R.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chin, S.M. et al., Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab. Nat Commun (2018)

Release Date

2018-11-21

Peptides

Utomilumab Fab heavy chain: A
Utomilumab Fab lambda chain: B
Tumor necrosis factor receptor superfamily member 9: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Utomilumab Fab heavy chain

Utomilumab Fab lambda chain

Tumor necrosis factor receptor superfamily member 9

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