SMTL ID : 5n8t.1

CRYSTAL STRUCTURE OF STREPTAVIDIN D-amino acid containing peptide Gdlwqheatwkkq

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x DLE: D-LEUCINE(Non-covalent)

DLE.1: 7 residues within 4Å: Chain A: L.49, S.51, Y.67 Ligands: DTR.2, DGN.3, DHI.4, DGL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.49, A:L.49 Hydrogen bonds: A:Y.67, A:Y.67

2 x DTR: D-TRYPTOPHAN(Non-covalent)

DTR.2: 14 residues within 4Å: Chain A: N.47, S.51, F.53, Y.67, W.103, T.114, W.116, W.132, D.152 Ligands: DLE.1, DGN.3, DHI.4, DGL.5, DAL.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.67, A:W.103, A:W.103, A:T.114 Hydrogen bonds: A:N.47, A:S.51, A:S.51, A:Y.67, A:D.152 pi-Stacking: A:W.116, A:W.116, A:W.132, A:W.132 DTR.8: 8 residues within 4Å: Chain A: R.108, N.109, A.110 Ligands: DHI.4, DGL.5, DAL.6, DTH.7, DLY.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.108, A:R.108 Water bridges: A:R.108, A:R.108

1 x DGN: D-GLUTAMINE(Non-covalent)

DGN.3: 7 residues within 4Å: Chain A: W.132 Ligands: DLE.1, DTR.2, DHI.4, DGL.5, DAL.6, DTH.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.47, A:N.47, A:N.47, A:Q.48

1 x DHI: D-HISTIDINE(Non-covalent)

DHI.4: 7 residues within 4Å: Ligands: DLE.1, DTR.2, DGN.3, DGL.5, DAL.6, DTH.7, DTR.8 No protein-ligand interaction detected (PLIP)

1 x DGL: D-GLUTAMIC ACID

DGL.5: 13 residues within 4Å: Chain A: Y.67, S.76, Y.78, W.103, R.108, A.110 Ligands: DLE.1, DTR.2, DGN.3, DHI.4, DAL.6, DTH.7, DTR.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.67, A:Y.78, A:W.103 Hydrogen bonds: A:Y.78 Water bridges: A:S.76, A:S.76 Salt bridges: A:R.108

1 x DAL: D-ALANINE

DAL.6: 10 residues within 4Å: Chain A: W.103, A.110, S.112, L.134 Ligands: DTR.2, DGN.3, DHI.4, DGL.5, DTH.7, DTR.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.103, A:L.134 Hydrogen bonds: A:S.112

1 x DTH: D-THREONINE

DTH.7: 7 residues within 4Å: Chain A: A.110 Ligands: DGN.3, DHI.4, DGL.5, DAL.6, DTR.8, DLY.9 No protein-ligand interaction detected (PLIP)

1 x DLY: D-LYSINE

DLY.9: 2 residues within 4Å: Ligands: DTH.7, DTR.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyamichev, V.I. et al., Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target. Sci Rep (2017)

Release Date

2017-10-04

Peptides

Streptavidin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Streptavidin

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