SMTL ID : 3wzq.1

Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.7 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x ZOF: 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid(Non-covalent)

ZOF.1: 16 residues within 4Å: Chain A: D.25, L.27, D.29, Y.45, W.81, A.88, S.90, T.92, W.94, W.110, L.112, S.114, D.130 Chain C: W.122, K.123 Ligands: ZOF.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.81, A:W.81, A:W.81, A:L.112 Hydrogen bonds: A:Y.45, A:S.90, A:S.90, A:D.130 Water bridges: A:D.29 Salt bridges: A:D.25, A:D.29, C:K.123 ZOF.2: 16 residues within 4Å: Chain B: D.25, L.27, D.29, Y.45, W.81, A.88, S.90, T.92, W.94, W.110, L.112, S.114, K.123, D.130 Chain D: W.122 Ligands: ZOF.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.81, B:W.81, B:W.81, B:L.112 Hydrogen bonds: B:S.90, B:S.90, B:D.130, B:D.130 Water bridges: B:D.25, B:D.25, B:D.29, B:L.126 Salt bridges: B:D.25, B:D.29 ZOF.3: 16 residues within 4Å: Chain A: W.122, K.123 Chain C: D.25, L.27, D.29, Y.45, W.81, A.88, S.90, T.92, W.94, W.110, L.112, S.114, L.126 Ligands: ZOF.1 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.81, C:W.81, C:W.81, C:L.126 Hydrogen bonds: C:Y.45, C:S.90, C:S.90, C:D.130 Water bridges: C:D.25, C:D.25, C:D.29 Salt bridges: C:D.25, C:D.29, A:K.123 ZOF.5: 16 residues within 4Å: Chain B: W.122, K.123 Chain D: D.25, L.27, D.29, Y.45, W.81, A.88, S.90, T.92, W.94, W.110, L.112, S.114, L.126 Ligands: ZOF.2 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.81, D:W.81, D:W.81, D:L.112, D:L.126 Hydrogen bonds: D:S.90, D:S.90, D:D.130, D:D.130 Water bridges: D:D.29 Salt bridges: D:D.25, D:D.29

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 7 residues within 4Å: Chain C: R.55, K.82, N.83, N.84 Chain D: D.38, S.64, A.65 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.64, C:A.52, C:K.82, C:N.84, C:N.84 P6G.6: 6 residues within 4Å: Chain C: S.64, A.65 Chain D: R.55, K.82, N.83, N.84 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.82, D:N.84, D:N.84, C:S.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawato, T. et al., Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J.Biochem. (2015)

Release Date

2015-02-18

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin

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