SMTL ID : 6cpr.1

Crystal structure of 4-1BBL/4-1BB complex in C2 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-3-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: F.120 Chain B: F.120 Chain C: F.118, G.119, F.120 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:F.120, A:F.120, B:F.120, B:F.120

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

CL.2: 2 residues within 4Å: Chain A: H.87, H.136 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: V.61, H.126 Chain C: S.40 Ligands: SO4.4 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: G.38 Chain B: R.92, H.126 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: V.21, L.22 Chain E: K.47 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: V.21 Chain D: K.47 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: V.21, L.22 Chain F: K.47 Ligand excluded by PLIP

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

SO4.4: 6 residues within 4Å: Chain A: R.92, L.125, H.126 Chain C: A.37, G.38 Ligands: CL.3 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.38, A:H.126, A:H.126 Water bridges: C:L.36, C:V.39 Salt bridges: A:R.92 SO4.5: 8 residues within 4Å: Chain A: Q.67, G.152, A.153 Chain B: A.98, A.99, L.100, A.101, R.123 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.101, A:Q.67 Salt bridges: B:R.123 SO4.8: 4 residues within 4Å: Chain B: A.37, G.38 Chain C: R.92, H.126 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:L.124, C:H.126, B:G.38, D:T.39, D:T.39 Salt bridges: C:R.92 SO4.10: 5 residues within 4Å: Chain A: H.126 Chain C: P.34, S.40, L.41, T.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.41 SO4.13: 1 residues within 4Å: Chain D: R.53 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.53 SO4.14: 2 residues within 4Å: Chain C: S.128 Chain D: N.17 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.17, D:N.17 Water bridges: C:R.92

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

NAG.11: 2 residues within 4Å: Chain D: V.124, N.127 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.127 NAG.16: 1 residues within 4Å: Chain E: N.127 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.127 NAG.17: 1 residues within 4Å: Chain F: N.127 No protein-ligand interaction detected (PLIP)

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

NA.15: 1 residues within 4Å: Chain D: P.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.28 NA.19: 4 residues within 4Å: Chain F: G.12, P.25, C.26, S.58 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.12, F:C.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bitra, A. et al., Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier. J. Biol. Chem. (2018)

Release Date

2018-05-09

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
D

E
F

F
E

Tumor necrosis factor ligand superfamily member 9

Tumor necrosis factor receptor superfamily member 9

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