SMTL ID : 2gh7.1

Epi-biotin complex with core streptavidin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 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: BTQ.2 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.5: 18 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: BTQ.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.67, B:W.67, B:W.67, B:L.98, C:W.108 Hydrogen bonds: B:S.15, B:Y.31, B:S.33, B:N.37, B:S.76, B:S.76, B:D.116 BTN.8: 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: BTQ.9 13 PLIP interactions: 13 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 BTN.12: 18 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: BTQ.13 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.67, D:W.67, D:W.67, D:L.98, A:W.108 Hydrogen bonds: D:S.15, D:S.33, D:N.37, D:S.76, D:S.76, D:D.116

4 x BTQ: EPI-BIOTIN(Non-covalent)

BTQ.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 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 BTQ.6: 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.96, L.98, D.116 Chain C: W.108 Ligands: BTN.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.67, B:W.67, B:W.67, B:L.98, C:W.108 Hydrogen bonds: B:S.15, B:Y.31, B:S.33, B:N.37, B:S.76, B:S.76, B:D.116 BTQ.9: 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.8 13 PLIP interactions: 13 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 BTQ.13: 17 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.96, L.98, D.116 Ligands: BTN.12 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.67, D:W.67, D:W.67, D:L.98, A:W.108 Hydrogen bonds: D:S.15, D:S.33, D:N.37, D:S.76, D:S.76, D:D.116

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: A.26, L.27, T.28, T.45, G.46 Chain B: T.45 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Water bridges: B:T.45, B:T.45, A:R.47 Hydrogen bonds: A:L.27, A:T.45, A:T.45, A:G.46, A:G.46 GOL.4: 5 residues within 4Å: Chain A: V.35, G.36 Chain D: N.106, W.108, K.109 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.36, D:N.106, D:K.109 Water bridges: A:A.34 GOL.7: 3 residues within 4Å: Chain B: E.39, S.40, Y.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.39, B:E.39 GOL.10: 6 residues within 4Å: Chain C: A.26, L.27, T.28, T.45, G.46 Chain D: T.45 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.27, C:T.45, C:T.45, C:G.46, C:G.46, D:T.45 Water bridges: C:R.47 GOL.11: 5 residues within 4Å: Chain B: N.106, W.108, K.109 Chain C: V.35, G.36 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.106, B:K.109, C:G.36 Water bridges: C:A.34 GOL.14: 3 residues within 4Å: Chain D: E.39, S.40, Y.71 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le Trong, I. et al., The high-resolution structure of (+)-epi-biotin bound to streptavidin. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-04-18

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin

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