SMTL ID : 1sri.2 (1 other biounit)

STRUCTURE-BASED DESIGN OF SYNTHETIC AZOBENZENE LIGANDS FOR STREPTAVIDIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-octamer

Ligands

8 x DMB: 2-((3',5'-DIMETHYL-4'-HYDROXYPHENYL)AZO)BENZOIC ACID(Non-covalent)

DMB.1: 16 residues within 4Å: Chain B: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain G: W.108 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.38, B:W.67, B:W.67, B:T.78, B:L.98, B:L.98 Hydrogen bonds: B:N.11, B:S.15, B:S.33, B:S.33, B:N.37, B:S.76 pi-Stacking: B:W.67, B:W.80, B:W.96, B:W.96 DMB.2: 14 residues within 4Å: Chain A: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, W.96, L.98, D.116 Chain H: W.108 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:A.38, A:W.67, A:W.67, A:A.74, A:L.98, H:W.108 Hydrogen bonds: A:N.11, A:S.15, A:Y.31, A:S.33, A:S.33, A:N.37, A:N.37, A:S.76 Water bridges: A:A.74 pi-Stacking: A:W.67, A:W.80, A:W.96, A:W.96 DMB.3: 16 residues within 4Å: Chain D: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 Chain E: W.108 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:A.38, D:W.67, D:W.67, D:T.78, D:L.98, D:L.98 Hydrogen bonds: D:N.11, D:S.15, D:S.33, D:S.33, D:N.37, D:S.76 pi-Stacking: D:W.67, D:W.80, D:W.96, D:W.96 DMB.4: 14 residues within 4Å: Chain C: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, W.96, L.98, D.116 Chain F: W.108 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:A.38, C:W.67, C:W.67, C:A.74, C:L.98, F:W.108 Hydrogen bonds: C:N.11, C:S.15, C:Y.31, C:S.33, C:S.33, C:N.37, C:N.37, C:S.76 Water bridges: C:A.74 pi-Stacking: C:W.67, C:W.80, C:W.96, C:W.96 DMB.5: 16 residues within 4Å: Chain C: W.108 Chain F: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:A.38, F:W.67, F:W.67, F:T.78, F:L.98, F:L.98 Hydrogen bonds: F:N.11, F:S.15, F:Y.31, F:S.33, F:S.33, F:N.37, F:S.76 pi-Stacking: F:W.67, F:W.80, F:W.96, F:W.96 DMB.6: 14 residues within 4Å: Chain D: W.108 Chain E: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, W.96, L.98, D.116 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:A.38, E:W.67, E:W.67, E:A.74, E:L.98, D:W.108 Hydrogen bonds: E:N.11, E:S.15, E:S.33, E:S.33, E:N.37, E:N.37, E:S.76 Water bridges: E:A.74 pi-Stacking: E:W.67, E:W.80, E:W.96, E:W.96 DMB.7: 16 residues within 4Å: Chain A: W.108 Chain H: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, D.116 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:A.38, H:W.67, H:W.67, H:T.78, H:L.98, H:L.98 Hydrogen bonds: H:N.11, H:S.15, H:Y.31, H:S.33, H:S.33, H:N.37, H:S.76 pi-Stacking: H:W.67, H:W.80, H:W.96, H:W.96 DMB.8: 14 residues within 4Å: Chain B: W.108 Chain G: N.11, S.15, Y.31, S.33, V.35, N.37, A.38, W.67, A.74, S.76, W.96, L.98, D.116 18 PLIP interactions: 1 interactions with chain B, 17 interactions with chain G Hydrophobic interactions: B:W.108, G:A.38, G:W.67, G:W.67, G:A.74, G:L.98 Hydrogen bonds: G:N.11, G:S.15, G:S.33, G:S.33, G:N.37, G:N.37, G:S.76 Water bridges: G:A.74 pi-Stacking: G:W.67, G:W.80, G:W.96, G:W.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weber, P.C. et al., Structure-Based Design of Synthetic Azobenzene Ligands for Streptavidin. J.Am.Chem.Soc. (1994)

Release Date

1994-11-01

Peptides

STREPTAVIDIN: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

STREPTAVIDIN

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