SMTL ID : 2y1l.2 (1 other biounit)

Caspase-8 in Complex with DARPin-8.4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x ILE- GLU- THR- ASP: AC-IETD-CHO(Non-covalent)

ILE-GLU-THR-ASP.1: 18 residues within 4Å: Chain A: R.43, R.45, S.101, H.102, G.103, Q.143, A.144, C.145 Chain B: V.35, S.36, Y.37, R.38, N.39, P.40, T.44, W.45, D.80 Ligands: EDO.4 22 PLIP interactions: 12 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.35, B:Y.37, B:Y.37, B:N.39, B:P.40 Hydrogen bonds: B:S.36, B:R.38, B:R.38, B:R.38, A:G.103, A:Q.143, A:C.145 Water bridges: B:R.38, A:R.43, A:R.43, A:D.44, A:N.46 Salt bridges: B:R.38, B:R.38, A:R.43, A:R.45, A:H.102

1 x ILE- GLU- THR- ASJ: N-(2-oxoethyl)-L-isoleucyl-L-alpha-glutamyl-N-[(1R)-2-carboxy-1-formylethyl]-L-threoninamide(Non-covalent)

ILE-GLU-THR-ASJ.2: 15 residues within 4Å: Chain C: R.43, R.45, S.101, H.102, G.103, Q.143, A.144, C.145, Y.150 Chain D: V.35, S.36, Y.37, R.38, P.40, T.44 20 PLIP interactions: 11 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:V.35, D:Y.37, C:Y.150 Hydrogen bonds: D:S.36, D:R.38, D:R.38, D:R.38, D:R.38, C:H.102, C:G.103, C:Q.143, C:C.145 Water bridges: D:R.38, D:R.38, C:N.46 Salt bridges: D:R.38, D:R.38, C:R.43, C:R.45, C:H.102

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

SO4.3: 5 residues within 4Å: Chain A: H.27, N.46, G.47, T.48, H.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.47, A:H.49 Salt bridges: A:H.27, A:H.49 SO4.5: 4 residues within 4Å: Chain A: K.9 Chain B: R.96, K.97 Chain D: Y.73 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.96, B:R.96 Salt bridges: B:R.96, B:K.97 SO4.6: 5 residues within 4Å: Chain C: H.27, N.46, G.47, T.48, H.49 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.45, C:G.47, C:T.48, C:H.49 Water bridges: C:N.46 Salt bridges: C:H.27, C:H.49

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain B: N.39, E.42, W.45, K.78 Ligands: ILE-GLU-THR-ASP.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.39, B:K.78 Water bridges: B:E.42, B:E.42 EDO.7: 7 residues within 4Å: Chain B: V.31, Q.90 Chain C: Y.119, T.122, S.123 Chain D: E.21, F.24 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:E.21, C:T.122, C:T.122, B:Q.90 Water bridges: D:T.94 EDO.8: 7 residues within 4Å: Chain C: D.88, N.91 Chain E: L.19, E.20, R.23, D.44, L.53 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:E.20, E:D.44, E:D.44 Water bridges: E:E.20, C:D.88 EDO.9: 5 residues within 4Å: Chain F: N.74, V.76, T.82, D.105, A.108 4 PLIP interactions: 4 interactions with chain F Water bridges: F:N.74, F:N.109, F:N.109, F:N.109 EDO.10: 4 residues within 4Å: Chain F: G.124, H.125, L.126, E.127 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:L.126, F:E.127 Water bridges: F:H.125, F:I.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroeder, T. et al., Caspase-8 in Complex with Darpin-8.4. To be Published

Release Date

2011-12-28

Peptides

Caspase-8 subunit p18: AC
Caspase-8: BD
DARPIN-8.4: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Caspase-8 subunit p18

Caspase-8

DARPIN-8.4

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