SMTL ID : 3x00.1

Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with bis iminobiotin long tail (Bis-IMNtail) at 1.3 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 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: 17 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, L.126, D.130 Chain D: W.122, K.123 Ligands: EDN.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.81, A:W.81, A:L.112, A:L.126 Hydrogen bonds: A:Y.45, A:S.90, A:S.90, A:W.110 Water bridges: A:Q.26, A:D.29 Salt bridges: A:D.25, A:D.29, A:D.130 ZOF.2: 17 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, L.126, D.130 Chain C: W.122, K.123 Ligands: EDN.3 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.81, B:W.81, B:W.81, B:L.112, B:L.126, C:W.122 Hydrogen bonds: B:S.90, B:S.90, B:W.110 Water bridges: B:Q.26, B:D.29 Salt bridges: B:D.25, B:D.29, B:D.130 ZOF.4: 17 residues within 4Å: Chain B: 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, D.130 Ligands: EDN.3 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.81, C:W.81, C:W.81, C:L.112, C:L.126 Hydrogen bonds: C:S.90, C:S.90, C:W.110 Water bridges: C:Q.26, C:D.29, C:D.29, B:K.123 Salt bridges: C:D.25, C:D.29, C:D.130 ZOF.5: 17 residues within 4Å: Chain A: 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, D.130 Ligands: EDN.6 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.81, D:W.81, D:W.81, D:L.112, D:L.126, A:W.122 Hydrogen bonds: D:Y.45, D:S.90, D:S.90, D:W.110 Water bridges: D:Q.26, D:D.29, D:D.29 Salt bridges: D:D.25, D:D.29, D:D.130

2 x EDN: ETHANE-1,2-DIAMINE

EDN.3: 4 residues within 4Å: Chain B: L.126 Chain C: L.126 Ligands: ZOF.2, ZOF.4 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:S.114, C:S.114, B:S.114 EDN.6: 4 residues within 4Å: Chain A: L.126 Chain D: L.126 Ligands: ZOF.1, ZOF.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Water bridges: A:S.114, D:S.114, D:S.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawato, T. et al., Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant. Biosci.Biotechnol.Biochem. (2015)

Release Date

2015-01-21

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin

Related Entries With Identical Sequence