SMTL ID : 3wyp.1

Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

2 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 C: W.108 Ligands: GOL.10 12 PLIP interactions: 12 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 BTN.9: 18 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 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:S.33, C:N.37, C:S.76, C:S.76, C:D.116

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Q.12, L.13, G.114, H.115 Chain C: W.108 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.12, A:H.115, A:H.115 GOL.3: 6 residues within 4Å: Chain A: G.14, S.15, T.16, E.32, S.33, A.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.16, A:T.16 GOL.4: 4 residues within 4Å: Chain A: H.115 Chain D: N.93, T.117 Ligands: GOL.2 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:T.117, A:H.115 Water bridges: A:H.115 GOL.6: 6 residues within 4Å: Chain B: Q.12, L.13, G.114, H.115, D.116 Chain D: W.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.12, B:H.115, B:H.115 GOL.7: 6 residues within 4Å: Chain B: G.14, S.15, T.16, E.32, S.33, A.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.16, B:T.16 GOL.10: 3 residues within 4Å: Chain A: L.112 Chain C: W.108 Ligands: BTN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.100 Water bridges: A:S.76 GOL.11: 5 residues within 4Å: Chain A: W.108 Chain C: Q.12, L.13, G.114, H.115 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.12, C:H.115, C:H.115 Water bridges: C:H.115 GOL.12: 6 residues within 4Å: Chain C: K.68, N.69, N.70 Chain D: D.24, R.47, S.50 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:K.68, C:N.70, D:R.47, D:S.50, D:S.50 Water bridges: C:K.68, D:D.24, D:S.50 GOL.14: 5 residues within 4Å: Chain B: W.108 Chain D: Q.12, L.13, G.114, H.115 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Water bridges: B:W.108 Hydrogen bonds: D:Q.12, D:H.115, D:H.115 GOL.15: 4 residues within 4Å: Chain B: W.108 Chain D: S.100, L.112 Ligands: BSO.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.76, D:S.100, D:S.100

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

BSO.5: 17 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 D: W.108 13 PLIP interactions: 13 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:D.116 pi-Cation interactions: B:W.96, B:W.96 BSO.13: 18 residues within 4Å: Chain B: 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.15 14 PLIP interactions: 14 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:Y.31, D:S.33, D:N.37, D:S.76, D:T.78, D:D.116 pi-Cation interactions: D:W.96, D:W.96

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

SO4.8: 3 residues within 4Å: Chain A: H.75 Chain B: A.53, T.54 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:H.75 Hydrogen bonds: B:T.54 Water bridges: B:T.54, B:D.55 SO4.16: 3 residues within 4Å: Chain D: A.53, T.54, D.55 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.54, D:T.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawato, T. et al., Crystal structure of streptavidin mutant with low immunogenicity. J.Biosci.Bioeng. (2015)

Release Date

2014-12-24

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

Streptavidin

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