SMTL ID : 2g5l.1

Streptavidin in complex with Nanotag

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-tetramer

Ligands

4 x FME- ASP- VAL- GLU- ALA- TRP- LEU: (FME)(ASP)(VAL)(GLU)(ALA)(TRP)(LEU)(Non-covalent)

FME-ASP-VAL-GLU-ALA-TRP-LEU.1: 17 residues within 4Å: Chain A: N.11, L.13, S.15, Y.31, S.33, A.34, Y.42, W.67, R.72, S.76, T.78, W.96, L.98, S.100, H.115, D.116 Chain D: W.108 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.13, A:Y.31, A:Y.42, A:W.67, D:W.108 Hydrogen bonds: A:N.11, A:S.15, A:S.15, A:A.34, A:S.76, A:D.116 Water bridges: A:S.15, D:A.105, D:K.109 FME-ASP-VAL-GLU-ALA-TRP-LEU.2: 15 residues within 4Å: Chain B: N.11, L.13, S.15, Y.31, Y.42, W.67, A.74, S.76, T.78, W.96, L.98, S.100, H.115, D.116 Chain C: W.108 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.31, B:W.67, B:W.67, B:W.67, B:L.98, B:L.98, C:W.108, C:W.108 Hydrogen bonds: B:S.15, B:S.15, B:S.76, B:D.116 Water bridges: B:H.115 pi-Stacking: B:W.67 FME-ASP-VAL-GLU-ALA-TRP-LEU.6: 17 residues within 4Å: Chain B: W.108 Chain C: N.11, L.13, S.15, Y.31, S.33, A.34, Y.42, W.67, R.72, S.76, T.78, W.96, L.98, S.100, H.115, D.116 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.13, C:Y.31, C:Y.42, C:W.67, B:W.108 Hydrogen bonds: C:N.11, C:S.15, C:S.15, C:Y.31, C:A.34, C:S.76, C:D.116 Water bridges: C:S.15, B:K.109 FME-ASP-VAL-GLU-ALA-TRP-LEU.7: 15 residues within 4Å: Chain A: W.108 Chain D: N.11, L.13, S.15, Y.31, Y.42, W.67, A.74, S.76, T.78, W.96, L.98, S.100, H.115, D.116 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain D Hydrophobic interactions: A:W.108, A:W.108, D:Y.31, D:W.67, D:W.67, D:W.67, D:L.98, D:L.98 Water bridges: A:A.105, D:H.115 Hydrogen bonds: D:S.15, D:S.15, D:S.76, D:D.116 pi-Stacking: D:W.67

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

SO4.3: 5 residues within 4Å: Chain A: G.22, A.23, D.24, G.25, A.26 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.22, A:A.23, A:D.24, A:D.24, A:G.25, A:A.26 Water bridges: A:R.47 SO4.5: 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:G.25, B:A.26 Water bridges: B:R.47 SO4.8: 5 residues within 4Å: Chain C: G.22, A.23, D.24, G.25, A.26 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.22, C:A.23, C:D.24, C:G.25, C:A.26 Water bridges: C:R.47 SO4.10: 5 residues within 4Å: Chain D: G.22, A.23, D.24, G.25, A.26 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.23, D:D.24, D:D.24, D:G.25, D:A.26 Water bridges: D:R.47

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: N.93, T.94, Q.95 Chain B: A.107, W.108, S.110, T.111 Chain C: V.113, G.114 9 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 5 interactions with chain A Water bridges: B:T.111, C:V.113, C:H.115, A:T.94, A:T.94, A:Q.95 Hydrogen bonds: C:V.113, A:T.94, A:Q.95 GOL.9: 9 residues within 4Å: Chain A: V.113, G.114 Chain C: N.93, T.94, Q.95 Chain D: A.107, W.108, S.110, T.111 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:V.113, C:T.94, C:Q.95 Water bridges: A:V.113, A:H.115, C:T.94, C:T.94, C:Q.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perbandt, M. et al., High resolution structure of Streptavidin in complex with a novel high affinity peptide tag mimicking the biotin binding motif. To be Published

Release Date

2007-02-06

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin

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