SMTL ID : 3t6f.1

Biotin complex of Y54F core streptavidin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-tetramer

Ligands

4 x BTN: BIOTIN(Non-covalent)

BTN.1: 19 residues within 4Å: Chain A: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain D: W.108 Ligands: BSO.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.38, A:W.67, A:W.67, A:W.67, A:L.98 Hydrogen bonds: A:N.11, A:S.15, A:S.33, A:N.37, A:S.76, A:S.76, A:D.116 Water bridges: A:N.37 BTN.5: 19 residues within 4Å: Chain B: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain C: W.108 Ligands: BSO.7, GOL.14 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.67, B:W.67, B:W.67, B:L.98 Hydrogen bonds: B:N.11, B:S.15, B:Y.31, B:S.33, B:N.37, B:S.76, B:S.76, B:D.116 BTN.12: 19 residues within 4Å: Chain B: W.108 Chain C: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: BSO.13 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.38, C:W.67, C:W.67, C:W.67, C:L.98 Hydrogen bonds: C:N.11, C:S.15, C:Y.31, C:S.33, C:N.37, C:S.76, C:S.76, C:D.116 Water bridges: C:N.37 BTN.16: 19 residues within 4Å: Chain A: W.108 Chain D: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: GOL.3, BSO.18 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.67, D:W.67, D:W.67, D:L.98 Hydrogen bonds: D:N.11, D:S.15, D:S.33, D:N.37, D:S.76, D:S.76, D:D.116

4 x BSO: BIOTIN-D-SULFOXIDE(Non-covalent)

BSO.2: 19 residues within 4Å: Chain A: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain D: W.108 Ligands: BTN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.38, A:W.67, A:W.67, A:W.67, A:L.98 Hydrogen bonds: A:N.11, A:S.15, A:S.33, A:N.37, A:S.76, A:T.78, A:D.116 Water bridges: A:N.37 pi-Cation interactions: A:W.96, A:W.96 BSO.7: 19 residues within 4Å: Chain B: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain C: W.108 Ligands: BTN.5, GOL.14 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.67, B:W.67, B:W.67, B:L.98 Hydrogen bonds: B:N.11, B:S.15, B:Y.31, B:S.33, B:N.37, B:S.76, B:T.78, B:D.116 pi-Cation interactions: B:W.96, B:W.96 BSO.13: 19 residues within 4Å: Chain B: W.108 Chain C: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: BTN.12 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.38, C:W.67, C:W.67, C:W.67, C:L.98 Hydrogen bonds: C:N.11, C:S.15, C:Y.31, C:S.33, C:N.37, C:S.76, C:D.116 Water bridges: C:N.37 pi-Cation interactions: C:W.96, C:W.96 BSO.18: 19 residues within 4Å: Chain A: W.108 Chain D: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Ligands: GOL.3, BTN.16 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.67, D:W.67, D:W.67, D:L.98 Hydrogen bonds: D:N.11, D:S.15, D:S.33, D:N.37, D:S.76, D:D.116 pi-Cation interactions: D:W.96, D:W.96

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain D: L.112 Ligands: BTN.16, BSO.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.37 GOL.4: 5 residues within 4Å: Chain A: V.35, G.36 Chain D: W.108, K.109 Ligands: GOL.21 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.36, D:K.109 GOL.10: 5 residues within 4Å: Chain B: K.109 Chain C: V.35, G.36, N.37 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.36 GOL.11: 2 residues within 4Å: Chain B: E.39, Y.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.39, B:E.39, B:Y.71 GOL.14: 3 residues within 4Å: Chain B: L.112 Ligands: BTN.5, BSO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 GOL.15: 5 residues within 4Å: Chain B: W.108, K.109 Chain C: V.35, G.36 Ligands: GOL.10 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.36, B:K.109 GOL.21: 5 residues within 4Å: Chain A: V.35, G.36, N.37 Chain D: K.109 Ligands: GOL.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.36 Water bridges: D:W.108 GOL.22: 2 residues within 4Å: Chain D: E.39, Y.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.39, D:Y.71

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain B: G.22, A.23, D.24, G.25, A.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.23, B:D.24, B:A.26 Water bridges: B:D.24, B:R.47 SO4.8: 2 residues within 4Å: Chain B: T.30, R.41 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.41 SO4.9: 2 residues within 4Å: Chain B: G.87, A.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.88 Water bridges: B:E.89 SO4.17: 5 residues within 4Å: Chain D: G.22, A.23, D.24, G.25, A.26 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.23, D:D.24, D:A.26 Water bridges: D:D.24, D:R.47 SO4.19: 2 residues within 4Å: Chain D: T.30, R.41 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.41 SO4.20: 2 residues within 4Å: Chain D: G.87, A.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.88 Water bridges: D:E.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Second-Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics. Biochemistry (2012)

Release Date

2011-12-21

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin

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