SMTL ID : 4j6g.1 (2 other biounits)

CRYSTAL STRUCTURE OF LIGHT AND DcR3 COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-6-6-mer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN.1: 10 residues within 4Å: Chain B: N.144, T.146 Chain L: P.25, Q.51, F.52, W.53, R.74, H.77, T.79, H.80 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:R.74, L:H.80, L:T.79 NAG-NAG-BMA-MAN.4: 10 residues within 4Å: Chain D: N.144, T.146 Chain H: P.25, Q.51, F.52, W.53, R.74, H.77, T.79, H.80 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:T.79, H:R.74, H:T.79 NAG-NAG-BMA-MAN.7: 10 residues within 4Å: Chain F: N.144, T.146 Chain J: P.25, Q.51, F.52, W.53, R.74, H.77, T.79, H.80 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.74, J:H.80, J:T.79

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

CL.2: 6 residues within 4Å: Chain A: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain C: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain E: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain G: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain I: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain K: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain B: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.103, B:A.107, B:S.130, B:S.132, H2O.1 MG.6: 6 residues within 4Å: Chain D: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.103, D:A.107, D:S.130, D:S.132, H2O.2 MG.9: 6 residues within 4Å: Chain F: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.103, F:A.107, F:S.130, F:S.132, H2O.3 MG.12: 6 residues within 4Å: Chain H: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.103, H:A.107, H:S.130, H:S.132, H2O.4 MG.15: 6 residues within 4Å: Chain J: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:C.103, J:A.107, J:S.130, J:S.132, H2O.5 MG.18: 6 residues within 4Å: Chain L: C.103, P.104, P.105, A.107, S.130, S.132 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:C.103, L:A.107, L:S.130, L:S.132, H2O.6

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

NAG.11: 6 residues within 4Å: Chain D: P.25, F.52, W.53 Chain H: N.144, T.146, A.147 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:T.146 Hydrophobic interactions: D:F.52 NAG.14: 6 residues within 4Å: Chain F: P.25, F.52, W.53 Chain J: N.144, T.146, A.147 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain J Hydrophobic interactions: F:F.52 Hydrogen bonds: J:T.146 NAG.17: 6 residues within 4Å: Chain B: P.25, F.52, W.53 Chain L: N.144, T.146, A.147 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly. Structure (2014)

Release Date

2013-03-13

Peptides

Tumor necrosis factor ligand superfamily member 14: ACEGIK
Tumor necrosis factor receptor superfamily member 6B: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
B

I
B

K
B

B
C

D
C

F
C

H
D

J
D

L
D

Tumor necrosis factor ligand superfamily member 14

Tumor necrosis factor receptor superfamily member 6B

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