SMTL ID : 6qsy.1

Engineered streptavidin variant (H--WY) in complex with the Strep-tag II peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-4-4-mer

Ligands

12 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 9 residues within 4Å: Chain A: G.29, T.30, R.41, Y.42, V.43, K.68, N.69, N.70 Chain G: D.24 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:T.30, A:R.41, A:K.68, A:N.70 Water bridges: A:V.43, A:N.70, G:R.47 PGE.3: 7 residues within 4Å: Chain A: L.98, S.100, Y.107, S.108, L.110 Chain E: L.110 Chain F: A.3 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.3 PGE.4: 4 residues within 4Å: Chain A: K.68 Chain G: A.23, S.50, A.51 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:A.23, G:S.50, A:K.68 PGE.5: 9 residues within 4Å: Chain C: G.29, T.30, R.41, Y.42, V.43, K.68, N.69, N.70 Chain E: D.24 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:T.30, C:R.41, C:K.68, C:N.70 Water bridges: C:V.43, C:N.70, E:R.47 PGE.7: 7 residues within 4Å: Chain C: L.98, S.100, Y.107, S.108, L.110 Chain G: L.110 Chain H: A.3 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:A.3, H:A.3 PGE.8: 4 residues within 4Å: Chain C: K.68 Chain E: A.23, S.50, A.51 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:K.68, E:A.23, E:S.50 PGE.9: 9 residues within 4Å: Chain C: D.24 Chain E: G.29, T.30, R.41, Y.42, V.43, K.68, N.69, N.70 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:T.30, E:R.41, E:K.68, E:N.70 Water bridges: E:V.43, E:N.70, C:R.47 PGE.11: 7 residues within 4Å: Chain A: L.110 Chain B: A.3 Chain E: L.98, S.100, Y.107, S.108, L.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.3 PGE.12: 4 residues within 4Å: Chain C: A.23, S.50, A.51 Chain E: K.68 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:K.68, C:A.23, C:S.50 PGE.13: 9 residues within 4Å: Chain A: D.24 Chain G: G.29, T.30, R.41, Y.42, V.43, K.68, N.69, N.70 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain G Water bridges: A:R.47, G:V.43, G:N.70 Hydrogen bonds: G:T.30, G:R.41, G:K.68, G:N.70 PGE.15: 7 residues within 4Å: Chain C: L.110 Chain D: A.3 Chain G: L.98, S.100, Y.107, S.108, L.110 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.3, D:A.3 PGE.16: 4 residues within 4Å: Chain A: A.23, S.50, A.51 Chain G: K.68 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:A.23, A:S.50, G:K.68

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: A.3, G.4, I.5, T.6, A.21 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.3, A:G.4, A:I.5, A:T.6, A:T.6 Water bridges: A:G.4, A:T.6 TRS.6: 5 residues within 4Å: Chain C: A.3, G.4, I.5, T.6, A.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.4, C:I.5, C:T.6, C:T.6 Water bridges: C:G.4, C:T.6 TRS.10: 5 residues within 4Å: Chain E: A.3, G.4, I.5, T.6, A.21 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:A.3, E:G.4, E:I.5, E:T.6, E:T.6 Water bridges: E:G.4, E:T.6 TRS.14: 5 residues within 4Å: Chain G: A.3, G.4, I.5, T.6, A.21 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:G.4, G:I.5, G:T.6, G:T.6 Water bridges: G:G.4, G:T.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, T.G.M. et al., The Role of Changing Loop Conformations in Streptavidin Versions Engineered for High-affinity Binding of the Strep-tag II Peptide. J.Mol.Biol. (2021)

Release Date

2020-03-18

Peptides

Streptavidin: ACEG
Strep-tag II peptide: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
P

D
P

F
P

H
P

Streptavidin

Strep-tag II peptide

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