SMTL ID : 8y27.1

X-ray crystal structure of ALiS5-Streptavidine complex with 10% glycerol using a high-pressure cryocooling method

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 7 residues within 4Å: Chain A: W.65, T.76, W.78, W.94, D.114 Chain C: W.106 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:D.114 pi-Cation interactions: A:W.94, A:W.94

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: V.33, G.34, N.35, A.36, W.65, A.72, S.74, L.96 Ligands: DMS.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.31, A:S.31, A:N.35, A:N.35 Water bridges: A:S.74 GOL.5: 8 residues within 4Å: Chain A: A.105, W.106, S.108 Chain C: W.94, V.111, G.112, H.113 Chain D: Q.93 8 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:V.111, C:H.113, C:H.113, A:S.108 Water bridges: C:Q.10, C:V.111, A:S.108, D:Q.81 GOL.6: 3 residues within 4Å: Chain A: W.106 Chain C: S.31 Ligands: 01.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.31

3 x 01: dimethyl 5-(4-oxidanylidene-5~{H}-furo[3,2-c]pyridin-2-yl)benzene-1,3-dicarboxylate

01.3: 13 residues within 4Å: Chain B: S.13, Y.29, S.31, Y.40, W.65, A.72, S.74, T.76, W.78, W.94, L.96, D.114 Chain D: W.106 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.65, B:T.76, B:W.94, B:L.96 Hydrogen bonds: B:S.13, B:Y.29, B:S.31, B:S.74, B:D.114 Water bridges: B:N.9 pi-Stacking: B:W.65, B:W.65 01.4: 15 residues within 4Å: Chain C: N.9, S.13, Y.29, S.31, Y.40, W.65, R.70, A.72, S.74, T.76, W.78, W.94, L.96, D.114 Ligands: GOL.6 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.65, C:T.76, C:W.94, C:L.96 Hydrogen bonds: C:N.9, C:S.13, C:Y.29, C:S.31, C:Y.40, C:S.74, C:D.114 Water bridges: C:Q.10 pi-Stacking: C:W.65, C:W.65, A:W.106 01.7: 14 residues within 4Å: Chain B: W.106 Chain D: N.9, S.13, Y.29, E.37, S.38, Y.40, W.65, R.70, A.72, S.74, W.78, W.94, D.114 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.65, B:W.106 Hydrogen bonds: D:N.9, D:S.13, D:D.114 Water bridges: D:R.70 Salt bridges: D:R.70, D:R.70 pi-Stacking: D:W.65

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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