SMTL ID : 8y25.1

X-ray crystal structure of ALiS4-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: S.31, V.33, N.35, W.65, A.72, S.74, L.96 Chain C: W.106 Ligands: DMS.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.31, A:S.31, A:N.35, A:S.74 Water bridges: A:S.98, A:S.98 GOL.3: 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: PEG.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.29, B:T.76, B:D.114 Water bridges: B:D.114 GOL.5: 10 residues within 4Å: Chain A: W.106 Chain C: S.31, V.33, G.34, N.35, A.36, W.65, S.74, L.96 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.31, C:S.31, C:N.35, C:S.74 GOL.6: 11 residues within 4Å: Chain A: W.106 Chain C: N.9, Y.29, V.33, W.65, T.76, W.78, W.94, L.96, D.114 Ligands: GOL.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.9, C:Y.29, C:T.76, C:T.76, C:W.78 Water bridges: C:Q.10, C:S.31, C:W.94, C:D.114 GOL.7: 9 residues within 4Å: Chain A: A.105, W.106, S.108, T.109 Chain C: W.94, V.111, G.112, H.113 Chain D: Q.93 10 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D, 4 interactions with chain A Hydrogen bonds: C:H.113, C:H.113, D:Q.93, A:A.105 Water bridges: C:Q.10, D:Q.81, D:Q.93, A:A.105, A:S.108, A:T.109 GOL.8: 8 residues within 4Å: Chain D: Y.29, W.65, T.76, W.78, W.94, L.96, D.114 Ligands: PEG.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.76, D:T.76, D:D.114 Water bridges: D:Q.10

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

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

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain B: W.65, L.96 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.31, B:S.31, B:S.31 PEG.9: 2 residues within 4Å: Chain D: W.65 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.74, D:S.74

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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