SMTL ID : 6ud6.2 (1 other biounit)

Spectroscopic and structural characterization of a genetically encoded direct sensor for protein-ligand interactions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Y.32, W.68, T.79, W.81, W.97, L.99, D.117 Ligands: GOL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32, A:T.79 Water bridges: A:N.12, A:N.12 GOL.2: 6 residues within 4Å: Chain A: W.68, A.75, S.77, T.79, L.99 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.34, A:Y.43 GOL.3: 6 residues within 4Å: Chain A: V.44, K.69, N.70, N.71 Chain B: D.25, R.48 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.25, B:R.48, A:K.69 GOL.5: 8 residues within 4Å: Chain B: Y.32, W.68, T.79, W.81, W.97, L.99, D.117 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.32, B:T.79, B:T.79 Water bridges: B:N.12, B:N.12 GOL.6: 3 residues within 4Å: Chain B: N.70, R.73, N.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.70 Water bridges: B:N.74 GOL.7: 7 residues within 4Å: Chain B: S.34, W.68, A.75, S.77, T.79, L.99 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.77 Water bridges: B:Y.43, B:Y.43 GOL.8: 8 residues within 4Å: Chain A: D.25, G.26, R.48, S.51 Chain B: V.44, K.69, N.70, N.71 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.69, B:N.71, A:D.25, A:R.48, A:S.51 Water bridges: A:D.25, A:S.51 GOL.10: 8 residues within 4Å: Chain C: Y.32, W.68, T.79, W.81, W.97, L.99, D.117 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.32, C:Y.32, C:T.79 Water bridges: C:N.12, C:N.12 GOL.11: 6 residues within 4Å: Chain C: W.68, A.75, S.77, T.79, L.99 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.34, C:Y.43 GOL.12: 6 residues within 4Å: Chain C: V.44, K.69, N.70, N.71 Chain D: D.25, R.48 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.25, D:R.48, C:K.69 GOL.14: 8 residues within 4Å: Chain D: Y.32, W.68, T.79, W.81, W.97, L.99, D.117 Ligands: GOL.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.32, D:T.79, D:T.79 Water bridges: D:N.12, D:N.12 GOL.15: 3 residues within 4Å: Chain D: N.70, R.73, N.74 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.70 Water bridges: D:N.74 GOL.16: 7 residues within 4Å: Chain D: S.34, W.68, A.75, S.77, T.79, L.99 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.77 Water bridges: D:Y.43, D:Y.43 GOL.17: 8 residues within 4Å: Chain C: D.25, G.26, R.48, S.51 Chain D: V.44, K.69, N.70, N.71 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.25, C:R.48, C:S.51, D:K.69, D:N.71 Water bridges: C:D.25, C:S.51

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: G.23, A.24, D.25, G.26, A.27 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: G.23, A.24, D.25, G.26, A.27 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain C: G.23, A.24, D.25, G.26, A.27 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: G.23, A.24, D.25, G.26, A.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gleason, P.R. et al., Structural Origins of Altered Spectroscopic Properties upon Ligand Binding in Proteins Containing a Fluorescent Noncanonical Amino Acid. Biochemistry (2021)

Release Date

2020-09-23

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin

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