SMTL ID : 5ygs.3 (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: 22 residues within 4Å: Chain A: N.13, D.15, K.16, K.43, E.45, E.46, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, G.261, M.331, S.338, W.341, Y.342, R.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.45, A:E.46, A:E.46, A:R.67, A:Y.342

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

SO4.2: 8 residues within 4Å: Chain A: P.383, A.384, R.385, R.386, W.387, K.388, R.412, Y.416 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.385, A:R.386, A:W.387, A:Y.416, A:Y.416 Salt bridges: A:R.412 SO4.3: 3 residues within 4Å: Chain A: G.14, H.40, D.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.42, A:D.42 Salt bridges: A:H.40 SO4.4: 2 residues within 4Å: Chain A: K.420, Q.424 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.420 SO4.5: 2 residues within 4Å: Chain A: Q.50, R.410 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.50 Salt bridges: A:R.410

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
C

Human TNRSF25 death domain

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