SMTL ID : 3x3f.1

TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 1 residues within 4Å: Chain A: N.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.73 Water bridges: A:S.75

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

CL.2: 4 residues within 4Å: Chain A: E.46, W.47 Chain B: T.97, F.98 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.176, H.177 Chain B: T.164, E.165, Q.166, D.167 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.176, B:E.165 Water bridges: A:T.178 GOL.4: 8 residues within 4Å: Chain A: G.42, Q.43, G.44 Chain B: A.9, V.85, Y.87, G.100, G.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.43 GOL.5: 11 residues within 4Å: Chain A: L.154, F.179, P.180, V.182, S.190, L.191, S.192 Chain B: Q.160, S.162, S.176, T.178 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:P.180, A:S.190, A:S.192, B:S.176, B:S.176, B:T.178 GOL.6: 2 residues within 4Å: Chain B: T.5, R.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.24 Water bridges: B:T.5, B:T.5, B:S.7, B:R.24 GOL.7: 7 residues within 4Å: Chain B: T.10, S.12, E.105, Y.140, P.141, R.142, Y.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.12, B:E.105, B:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamada, T. et al., TRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2. Sci Rep (2015)

Release Date

2015-12-23

Peptides

Heavy chain of KMTR2: A
Light chain of KMTR2: B
Tumor necrosis factor receptor superfamily member 10B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

Heavy chain of KMTR2

Light chain of KMTR2

Tumor necrosis factor receptor superfamily member 10B

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