SMTL ID : 4cpi.3 (2 other biounits)

streptavidin A86D mutant with love-hate ligand 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-tetramer

Ligands

4 x LH4: 5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4- d]imidazolidin-4-yl]-N'-{2,6-bis[4-(morpholine-4- sulfonyl)phenyl]phenyl}pentanehydrazide(Non-covalent)

LH4.1: 14 residues within 4Å: Chain A: N.11, L.13, S.15, Y.31, S.33, W.67, D.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain D: W.108 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.67, A:W.67, A:W.67, A:L.98 Hydrogen bonds: A:N.11, A:S.15, A:Y.31, A:S.33, A:S.76, A:D.116 Water bridges: D:K.109 LH4.2: 14 residues within 4Å: Chain B: N.11, L.13, S.15, Y.31, S.33, W.67, D.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain C: W.108 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.67, B:W.67, B:W.67, B:L.98 Hydrogen bonds: B:N.11, B:S.15, B:S.33, B:S.76, B:D.116 Water bridges: C:K.109 LH4.3: 19 residues within 4Å: Chain B: W.108 Chain C: N.11, L.13, S.15, Y.31, S.33, A.34, Y.42, W.67, Y.71, R.72, N.73, D.74, T.78, W.80, W.96, L.98, D.116 Ligands: PEG.4 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.67, C:W.67, C:R.72, C:R.72, C:L.98, B:W.108 Hydrogen bonds: C:N.11, C:S.15, C:S.33, C:A.34, C:Y.42, C:R.72, C:N.73, C:D.74, C:D.116 Water bridges: C:Y.42, C:Y.42 LH4.7: 19 residues within 4Å: Chain A: W.108 Chain D: N.11, L.13, S.15, Y.31, S.33, A.34, Y.42, W.67, Y.71, R.72, N.73, D.74, T.78, W.80, W.96, L.98, D.116 Ligands: PEG.8 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.67, D:W.67, D:R.72, D:R.72, D:L.98, A:W.108 Hydrogen bonds: D:N.11, D:S.15, D:Y.31, D:S.33, D:A.34, D:R.72, D:N.73, D:D.74, D:D.74, D:D.116 Water bridges: D:Y.42, D:Y.42, D:Y.42

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

PEG.4: 5 residues within 4Å: Chain B: K.109 Chain C: D.74 Ligands: LH4.3, PEG.5, CA.6 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.74, B:K.109, B:K.109 PEG.5: 5 residues within 4Å: Chain C: D.74, S.100, L.112 Ligands: PEG.4, CA.6 No protein-ligand interaction detected (PLIP) PEG.8: 5 residues within 4Å: Chain A: K.109 Chain D: D.74 Ligands: LH4.7, PEG.9, CA.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.109, A:K.109, D:D.74 PEG.9: 5 residues within 4Å: Chain D: D.74, S.100, L.112 Ligands: PEG.8, CA.10 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-functional Binders)

CA.6: 2 residues within 4Å: Ligands: PEG.4, PEG.5 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Ligands: PEG.8, PEG.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fairhead, M. et al., Love-Hate Ligands for High Resolution Analysis of Strain in Ultra-Stable Protein/Small Molecule Interaction. Bioorg.Med.Chem. (2014)

Release Date

2014-08-06

Peptides

STREPTAVIDIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
D

D
D

STREPTAVIDIN

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