SMTL ID : 8y29.1

X-ray crystal structure of ALiS2-Streptavidine complex without cryo-protectant using a high-pressure cryocooling method

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-tetramer

Ligands

4 x MT6: methyl 3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzoate(Non-covalent)

MT6.1: 17 residues within 4Å: Chain A: N.9, S.13, Y.29, S.31, V.33, N.35, A.36, W.65, A.72, S.74, T.76, W.78, W.94, L.96, S.98, D.114 Chain C: W.106 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.33, A:A.36, A:W.65, A:A.72, A:T.76, A:L.96 Hydrogen bonds: A:N.9, A:S.13, A:Y.29, A:S.74, A:D.114 Water bridges: A:N.35 pi-Stacking: A:W.65, A:W.65, A:W.78, A:W.94, A:W.94, C:W.106 MT6.2: 14 residues within 4Å: Chain B: N.9, S.13, Y.29, S.31, W.65, A.72, S.74, T.76, W.78, W.94, L.96, S.98, D.114 Chain D: W.106 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.65, B:A.72, B:T.76, B:L.96, D:W.106 Hydrogen bonds: B:N.9, B:S.13, B:Y.29, B:S.74, B:D.114 pi-Stacking: B:W.65, B:W.65, B:W.78, B:W.94, B:W.94, D:W.106 MT6.3: 14 residues within 4Å: Chain A: W.106 Chain C: N.9, S.13, Y.29, S.31, W.65, A.72, S.74, T.76, W.78, W.94, L.96, S.98, D.114 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.65, C:T.76, C:L.96 Hydrogen bonds: C:N.9, C:S.13, C:Y.29, C:D.114 Water bridges: C:Q.10 pi-Stacking: C:W.65, C:W.65, C:W.78, C:W.94, C:W.94, A:W.106 MT6.4: 13 residues within 4Å: Chain D: N.9, S.13, Y.29, Y.40, W.65, R.70, A.72, S.74, T.76, W.78, W.94, L.96, D.114 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.65, D:A.72, D:T.76, D:L.96 Hydrogen bonds: D:N.9, D:S.13, D:Y.40, D:D.114 Salt bridges: D:R.70 pi-Stacking: D:W.65, D:W.65, D:W.78, D:W.94, D:W.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higashiura, A. et al., Binding competition between substrates and cryoprotectants in protein crystals directly observed by a hybrid method of in-gel crystallization and high-pressure cryo-cooling in X-ray crystallography. To Be Published

Release Date

2025-01-29

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin

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