SMTL ID : 3wzo.1

Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin long tail (BTNtail) at 1.5 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

ZOE.1: 16 residues within 4Å: Chain A: D.17, Y.33, S.35, V.37, G.38, N.39, W.69, A.76, S.78, T.80, W.98, L.100, S.102, D.118 Chain D: W.110, K.111 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.69, A:W.69, A:W.69 Hydrogen bonds: A:Y.33, A:S.35, A:N.39, A:S.78, A:S.78, A:D.118 pi-Cation interactions: A:W.98 Salt bridges: D:K.111 ZOE.7: 17 residues within 4Å: Chain B: D.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.98, L.100, S.102, D.118 Chain C: W.110, K.111 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.40, B:W.69, B:W.69, B:W.69 Hydrogen bonds: B:S.35, B:N.39, B:S.78, B:S.78, B:T.80, B:D.118 pi-Stacking: B:W.98 pi-Cation interactions: B:W.98 Salt bridges: C:K.111 ZOE.9: 18 residues within 4Å: Chain B: W.110, K.111 Chain C: D.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.98, L.100, S.102, L.114, D.118 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.40, C:W.69, C:W.69, C:W.69, C:L.114, B:K.111 Hydrogen bonds: C:S.35, C:N.39, C:S.78, C:S.78, C:T.80, C:D.118 pi-Cation interactions: C:W.98 Water bridges: B:K.111 Salt bridges: B:K.111 ZOE.12: 16 residues within 4Å: Chain A: W.110 Chain D: D.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.98, L.100, S.102, D.118 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.40, D:W.69, D:W.69, D:W.69, D:L.100 Hydrogen bonds: D:Y.33, D:S.35, D:N.39, D:S.78, D:S.78, D:D.118 pi-Cation interactions: D:W.98 Salt bridges: A:K.111

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.4, G.24, A.25, D.26, Y.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.25, A:D.26, A:Y.50 GOL.10: 3 residues within 4Å: Chain C: I.20, G.31, T.32 No protein-ligand interaction detected (PLIP) GOL.13: 5 residues within 4Å: Chain D: E.4, G.24, A.25, D.26, Y.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.25, D:D.26, D:Y.50

9 x CD: CADMIUM ION(Non-covalent)

CD.3: 1 residues within 4Å: Chain A: D.91 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.91, A:D.91, H2O.2, H2O.2 CD.4: 2 residues within 4Å: Chain A: E.4, S.52 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.4, A:E.4, A:S.52, H2O.2 CD.5: 1 residues within 4Å: Chain A: E.34 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.34, A:E.34, H2O.3 CD.8: 2 residues within 4Å: Chain B: E.4, S.52 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.4, B:E.4, B:S.52, H2O.4, H2O.4 CD.11: 1 residues within 4Å: Chain C: H.77 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.77, H2O.6, H2O.9 CD.14: 1 residues within 4Å: Chain D: H.77 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.77, H2O.8, H2O.9, H2O.9 CD.15: 2 residues within 4Å: Chain D: E.4, S.52 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.4, D:E.4, D:S.52, H2O.8 CD.16: 1 residues within 4Å: Chain D: E.34 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.34, D:E.34 CD.17: 1 residues within 4Å: Chain D: D.91 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.91, D:D.91, H2O.9, H2O.9

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

P6G.6: 12 residues within 4Å: Chain A: G.6, S.59, G.60, T.61, Y.86, V.87, G.88, G.89, A.90, A.92, K.122, K.124 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.61, A:G.88, A:G.89 Water bridges: A:A.92, A:K.122 P6G.18: 9 residues within 4Å: Chain D: S.59, T.61, Y.86, V.87, G.88, G.89, A.90, A.92, K.122 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.61, D:Y.86, D:G.88, D:G.89 Water bridges: D:K.122

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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