SMTL ID : 6mgp.1

Structure of human 4-1BB / 4-1BBL complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 2 residues within 4Å: Chain D: W.112, N.125 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG-FUC.2: 3 residues within 4Å: Chain E: F.98, W.112, N.125 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG-FUC.3: 2 residues within 4Å: Chain F: V.122, N.125 No protein-ligand interaction detected (PLIP)

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

ACT.4: 5 residues within 4Å: Chain A: N.42, V.43, L.44 Chain D: Q.43, K.45 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:K.45, A:V.43 Salt bridges: D:K.45 Hydrogen bonds: A:V.43, A:L.44 ACT.5: 6 residues within 4Å: Chain A: Q.37, G.60, V.61, S.62 Chain C: L.146, H.148 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.37, A:G.60, A:S.62 Water bridges: A:V.61 Salt bridges: C:H.148 ACT.8: 4 residues within 4Å: Chain C: N.42, V.43, L.44 Chain F: K.45 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:V.43, C:L.44, C:L.44 Salt bridges: F:K.45 ACT.9: 6 residues within 4Å: Chain A: P.56 Chain D: C.13, D.14, N.15, N.16, R.36 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:N.15 Hydrogen bonds: D:N.15, A:P.56 ACT.10: 5 residues within 4Å: Chain B: Q.173 Chain E: I.40, C.41, R.42, N.59 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:N.59, E:N.59 Salt bridges: E:R.42 Hydrophobic interactions: B:Q.173

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: T.125, D.127 Chain B: R.136, N.137, S.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.137, B:S.138 GOL.7: 8 residues within 4Å: Chain A: F.140, G.141, F.142 Chain B: F.140, G.141, F.142 Chain C: F.140, F.142 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:F.142, C:F.142, C:F.142, A:F.142 GOL.11: 5 residues within 4Å: Chain C: Q.41, Y.53 Chain F: N.27, Q.43, K.45 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.41, C:Y.53, F:K.45, F:K.45 GOL.12: 5 residues within 4Å: Chain F: C.64, T.65, G.67, F.68, D.81 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:C.64, F:G.67, F:D.81 Water bridges: F:C.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimberlin, C.R. 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

2018-11-14

Peptides

Tumor necrosis factor ligand superfamily member 9: ABC
Tumor necrosis factor receptor superfamily member 9: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
X

E
Y

F
Z

Tumor necrosis factor ligand superfamily member 9

Tumor necrosis factor receptor superfamily member 9

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