SMTL ID : 4gda.1

Circular Permuted Streptavidin A50/N49

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-tetramer

Ligands

4 x BTN: BIOTIN(Non-covalent)

BTN.1: 18 residues within 4Å: Chain A: W.30, A.37, S.39, T.41, W.43, W.59, L.61, D.79, N.105, L.107, S.109, Y.125, S.127, V.129, G.130, N.131 Chain D: W.71 Ligands: GOL.15 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.30, A:W.30, A:W.30, A:L.61 Hydrogen bonds: A:S.39, A:S.39, A:D.79, A:N.105, A:S.109, A:S.127, A:N.131 BTN.5: 18 residues within 4Å: Chain B: W.30, A.37, S.39, T.41, W.43, W.59, L.61, D.79, N.105, L.107, S.109, Y.125, S.127, V.129, G.130, N.131 Chain C: W.71 Ligands: GOL.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.30, B:W.30, B:W.30, B:L.61 Hydrogen bonds: B:S.39, B:S.39, B:D.79, B:N.105, B:S.109, B:Y.125, B:S.127, B:N.131 BTN.10: 18 residues within 4Å: Chain B: W.71 Chain C: W.30, A.37, S.39, T.41, W.43, W.59, L.61, D.79, N.105, L.107, S.109, Y.125, S.127, V.129, G.130, N.131 Ligands: GOL.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:L.61 Hydrogen bonds: C:S.39, C:S.39, C:D.79, C:N.105, C:S.109, C:Y.125, C:S.127, C:N.131 Water bridges: C:N.131 BTN.14: 18 residues within 4Å: Chain A: W.71 Chain D: W.30, A.37, S.39, T.41, W.43, W.59, L.61, D.79, N.105, L.107, S.109, Y.125, S.127, V.129, G.130, N.131 Ligands: GOL.2 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.30, D:W.30, D:W.30, D:L.61 Hydrogen bonds: D:S.39, D:S.39, D:D.79, D:N.105, D:S.109, D:S.127, D:N.131 Water bridges: D:N.131

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: W.71, K.72 Chain D: L.61, L.75 Ligands: BTN.14 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Water bridges: D:S.39, D:S.63, D:S.63, D:N.131, A:K.72 GOL.3: 3 residues within 4Å: Chain A: K.31, N.33 Chain B: D.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.33 Water bridges: A:K.31 GOL.6: 5 residues within 4Å: Chain B: W.71, K.72 Chain C: L.61, L.75 Ligands: BTN.10 5 PLIP interactions: 5 interactions with chain C Water bridges: C:S.39, C:S.63, C:S.63, C:S.63, C:N.131 GOL.11: 5 residues within 4Å: Chain B: L.61, L.75 Chain C: W.71, K.72 Ligands: BTN.5 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Water bridges: C:K.72, B:S.39, B:S.63, B:S.63, B:N.131 GOL.12: 3 residues within 4Å: Chain C: K.31, N.33 Chain D: D.118 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.33 GOL.15: 5 residues within 4Å: Chain A: L.61, L.75 Chain D: W.71, K.72 Ligands: BTN.1 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.39, A:S.63, A:S.63, A:S.63, A:N.131

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

SO4.4: 3 residues within 4Å: Chain A: A.1, N.33, Y.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.1, A:N.33, A:Y.34 SO4.7: 1 residues within 4Å: Chain B: R.35 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.35 SO4.8: 4 residues within 4Å: Chain B: E.2, S.3, Y.34, R.35 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.5 Salt bridges: B:R.35 SO4.13: 3 residues within 4Å: Chain C: A.1, N.33, Y.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.33 Water bridges: C:A.1 SO4.16: 1 residues within 4Å: Chain D: R.35 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.35 SO4.17: 4 residues within 4Å: Chain D: E.2, S.3, Y.34, R.35 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.35

2 x EOH: ETHANOL(Non-functional Binders)

EOH.9: 5 residues within 4Å: Chain B: G.116, A.117, D.118, G.119, A.120 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.120 Hydrogen bonds: B:D.118, B:A.120 EOH.18: 5 residues within 4Å: Chain D: G.116, A.117, D.118, G.119, A.120 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.120 Hydrogen bonds: D:D.118, D:A.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le Trong, I. et al., Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-06-05

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin