SMTL ID : 5ygs.1 (3 other biounits)

Human TNFRSF25 death domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-functional Binders)

GLC-GLC-GLC.1: 19 residues within 4Å: Chain A: N.13, D.15, K.16, E.45, E.46, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, Y.342, R.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.46, A:W.63, A:R.67, A:W.341

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

SO4.2: 9 residues within 4Å: Chain A: A.384, R.385, R.386, W.387, K.388, R.412, D.413, Y.416, R.439 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.385, A:R.386, A:W.387, A:Y.416 Salt bridges: A:R.412 SO4.3: 2 residues within 4Å: Chain A: K.420, Q.424 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.424 SO4.4: 3 residues within 4Å: Chain A: P.41, D.42, K.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.42 Salt bridges: A:K.47 SO4.5: 7 residues within 4Å: Chain A: L.77, A.78, E.79, A.269, K.274, G.429, L.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.79 Salt bridges: A:K.274 SO4.6: 1 residues within 4Å: Chain A: T.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, X. et al., Crystal structure and activation mechanism of DR3 death domain. Febs J. (2019)

Release Date

2018-10-03

Peptides

Human TNRSF25 death domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Human TNRSF25 death domain

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