SMTL ID : 6mi2.1 (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

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

SO4.1: 5 residues within 4Å: Chain A: E.1, V.2, Y.105 Chain C: A.73, G.74 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:V.2, A:Y.105, C:G.74 SO4.2: 5 residues within 4Å: Chain A: S.25, G.26, Y.27, S.77 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.26, A:Y.27, A:Y.27, A:S.77 SO4.3: 3 residues within 4Å: Chain A: K.87, A.88, S.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.88, A:S.89, A:S.89 SO4.5: 5 residues within 4Å: Chain B: E.82, V.107, G.109, Q.110, Y.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.109, B:Q.110, B:Y.142, B:Y.142 SO4.6: 1 residues within 4Å: Chain B: R.53 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.53 SO4.7: 3 residues within 4Å: Chain B: K.38, Q.41 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.41, B:Q.41 Salt bridges: B:K.38 SO4.8: 3 residues within 4Å: Chain B: K.112, A.113, A.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.114 SO4.9: 2 residues within 4Å: Chain B: W.150, P.156 No protein-ligand interaction detected (PLIP) SO4.14: 3 residues within 4Å: Chain C: C.44, R.49, T.50 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.50, C:T.50 SO4.15: 6 residues within 4Å: Chain B: S.55 Chain C: R.42, Q.43, C.44, K.45, F.48 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.55, B:S.55, C:Q.43, C:C.44, C:K.45 Water bridges: B:G.56 Salt bridges: C:R.42 SO4.16: 2 residues within 4Å: Chain C: S.55, S.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.56 SO4.17: 3 residues within 4Å: Chain C: Q.80, G.92, C.93 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.80, C:C.93 SO4.18: 2 residues within 4Å: Chain C: R.49, P.66 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.49 SO4.19: 2 residues within 4Å: Chain C: N.15 Ligands: GOL.20 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.28, F.29, S.30, S.77 Ligands: SO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.27, A:F.29, A:S.30, A:S.77 Water bridges: A:S.28, A:S.28 GOL.10: 10 residues within 4Å: Chain A: G.42, K.43, G.44 Chain B: P.8, D.84, Y.86, G.101, G.102, T.103, K.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.8, B:D.84 GOL.11: 4 residues within 4Å: Chain B: L.108, G.109, Q.110, P.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.109 GOL.12: 7 residues within 4Å: Chain B: Q.36, K.38, P.58, F.61, M.80, D.81 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.36, B:K.38, B:M.80 GOL.20: 2 residues within 4Å: Chain C: R.36 Ligands: SO4.19 No protein-ligand interaction detected (PLIP) GOL.21: 3 residues within 4Å: Chain A: Y.32 Chain C: H.69, C.70 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:F.68, C:C.70, A:Y.32 GOL.22: 3 residues within 4Å: Chain C: K.120, S.137, N.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.137 Water bridges: C:K.120

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

NAG.13: 3 residues within 4Å: Chain C: V.122, L.123, N.125 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.125, C:N.125

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
A

B
B

C
C

Utomilumab Fab heavy chain

Utomilumab Fab lambda chain

Tumor necrosis factor receptor superfamily member 9

Related Entries With Identical Sequence