SMTL ID : 4dve.4 (3 other biounits)

Crystal structure at 2.1 A of the S-component for biotin from an ECF-type ABC transporter

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-hexamer

Ligands

6 x BTN: BIOTIN(Non-covalent)

BTN.1: 14 residues within 4Å: Chain A: V.46, P.47, I.48, I.49, N.52, L.85, S.99, Y.102, R.103, W.106, D.144, F.169, D.173, K.176 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.46, A:I.49, A:Y.102, A:R.103 Hydrogen bonds: A:P.47, A:I.49, A:N.52, A:T.86, A:S.99, A:S.99, A:D.173, A:K.176 Water bridges: A:D.173 Salt bridges: A:R.103 pi-Stacking: A:F.169 BTN.5: 15 residues within 4Å: Chain B: V.46, P.47, I.48, I.49, N.52, L.85, T.86, S.99, Y.102, R.103, W.106, D.144, F.169, D.173, K.176 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.46, B:R.103 Hydrogen bonds: B:P.47, B:I.49, B:N.52, B:T.86, B:S.99, B:D.173, B:K.176 Water bridges: B:D.173 Salt bridges: B:R.103 pi-Stacking: B:F.169 BTN.8: 15 residues within 4Å: Chain C: V.46, P.47, I.48, I.49, N.52, L.85, T.86, S.99, Y.102, R.103, W.106, D.144, F.169, D.173, K.176 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.46 Hydrogen bonds: C:P.47, C:I.49, C:N.52, C:T.86, C:S.99, C:S.99, C:D.173, C:K.176 Water bridges: C:D.173 Salt bridges: C:R.103 pi-Stacking: C:F.169 BTN.10: 14 residues within 4Å: Chain D: V.46, P.47, I.48, I.49, N.52, L.85, S.99, Y.102, R.103, W.106, D.144, F.169, D.173, K.176 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.46, D:I.49, D:Y.102, D:R.103 Hydrogen bonds: D:P.47, D:I.49, D:N.52, D:T.86, D:S.99, D:S.99, D:D.173, D:K.176 Water bridges: D:D.173 Salt bridges: D:R.103 pi-Stacking: D:F.169 BTN.14: 15 residues within 4Å: Chain E: V.46, P.47, I.48, I.49, N.52, L.85, T.86, S.99, Y.102, R.103, W.106, D.144, F.169, D.173, K.176 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.46, E:R.103 Hydrogen bonds: E:P.47, E:I.49, E:N.52, E:T.86, E:S.99, E:D.173, E:K.176 Water bridges: E:D.173 Salt bridges: E:R.103 pi-Stacking: E:F.169 BTN.17: 15 residues within 4Å: Chain F: V.46, P.47, I.48, I.49, N.52, L.85, T.86, S.99, Y.102, R.103, W.106, D.144, F.169, D.173, K.176 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:V.46 Hydrogen bonds: F:P.47, F:I.49, F:N.52, F:T.86, F:S.99, F:S.99, F:D.173, F:K.176 Water bridges: F:D.173 Salt bridges: F:R.103 pi-Stacking: F:F.169

12 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.2: 16 residues within 4Å: Chain A: L.20, S.23, A.24, T.27, A.28, I.31, I.69, S.70, A.73 Chain C: L.20, S.23, A.24, T.27, I.31, S.70, A.73 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.28, A:I.31, C:T.27, C:I.31 Hydrogen bonds: A:T.27, A:T.27, C:S.70 Water bridges: A:S.23 BNG.3: 8 residues within 4Å: Chain A: P.64, K.65, T.68, I.69, F.111, F.115, K.118 Chain C: L.20 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:K.65, A:T.68, A:I.69, C:L.20 Hydrogen bonds: A:K.118, A:K.118 BNG.4: 6 residues within 4Å: Chain A: G.81, P.83, G.88, G.90, G.91 Chain C: I.32 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.83, C:I.32 Hydrogen bonds: A:G.90 Water bridges: A:G.90 BNG.6: 17 residues within 4Å: Chain B: S.23, A.24, T.27, I.31, S.70, A.73 Chain E: L.20, S.23, A.24, T.27, A.28, I.31, F.35, I.69, S.70, A.73 Ligands: BNG.15 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:T.27, E:A.28, E:I.31, E:F.35, B:I.31 Hydrogen bonds: E:S.23, E:S.23, B:T.27 BNG.7: 7 residues within 4Å: Chain B: K.65, T.68, G.72, F.111, F.115, K.118 Chain E: L.20 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:L.20 Hydrogen bonds: B:K.118, B:K.118 BNG.9: 6 residues within 4Å: Chain C: K.65, T.68, I.69, F.111, F.115, K.118 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.68, C:I.69 Hydrogen bonds: C:K.118 BNG.11: 16 residues within 4Å: Chain D: L.20, S.23, A.24, T.27, A.28, I.31, I.69, S.70, A.73 Chain F: L.20, S.23, A.24, T.27, I.31, S.70, A.73 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:T.27, F:I.31, D:A.28, D:I.31 Hydrogen bonds: F:T.27, F:S.70, D:T.27 Water bridges: D:S.23 BNG.12: 8 residues within 4Å: Chain D: P.64, K.65, T.68, I.69, F.111, F.115, K.118 Chain F: L.20 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain D Hydrophobic interactions: F:L.20, D:K.65, D:T.68, D:I.69 Hydrogen bonds: D:K.118, D:K.118 BNG.13: 6 residues within 4Å: Chain D: G.81, P.83, G.88, G.90, G.91 Chain F: I.32 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:P.83, F:I.32 Hydrogen bonds: D:G.90 Water bridges: D:G.90 BNG.15: 17 residues within 4Å: Chain B: L.20, S.23, A.24, T.27, A.28, I.31, F.35, I.69, S.70, A.73 Chain E: S.23, A.24, T.27, I.31, S.70, A.73 Ligands: BNG.6 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:T.27, B:A.28, B:I.31, B:F.35, E:I.31 Hydrogen bonds: B:S.23, B:S.23, B:T.27 BNG.16: 7 residues within 4Å: Chain B: L.20 Chain E: K.65, T.68, G.72, F.111, F.115, K.118 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:L.20 Hydrogen bonds: E:K.118, E:K.118 BNG.18: 6 residues within 4Å: Chain F: K.65, T.68, I.69, F.111, F.115, K.118 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.68, F:I.69 Hydrogen bonds: F:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berntsson, R.P. et al., Structural divergence of paralogous S components from ECF-type ABC transporters. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-08-29

Peptides

Biotin transporter BioY: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Biotin transporter BioY

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