SMTL ID : 8y2b.1

X-ray crystal structure of ALiS2-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

MT6.1: 16 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, D.114 Chain C: W.106 17 PLIP interactions: 17 interactions with chain A 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:S.98 pi-Stacking: A:W.65, A:W.65, A:W.78, A:W.94, A:W.94 MT6.4: 16 residues within 4Å: Chain C: 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 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.33, C:A.36, 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain B: Y.29, W.65, T.76, W.78, W.94, L.96, D.114 Chain D: W.106 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.9, B:Y.29, B:T.76, B:D.114 Water bridges: B:S.31, B:D.114 GOL.3: 4 residues within 4Å: Chain B: S.31, W.65, L.96 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.31, B:S.74, B:S.74 GOL.5: 8 residues within 4Å: Chain B: W.106 Chain D: N.9, W.65, T.76, W.78, W.94, L.96, D.114 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.9, D:Y.29, D:T.76, D:T.76

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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