SMTL ID : 2hvk.1

crystal structure of the KcsA-Fab-TBA complex in high K+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x F09: NONAN-1-OL(Non-covalent)

F09.1: 4 residues within 4Å: Chain A: R.57 Chain C: L.46, W.87, V.91 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.46, C:V.91 F09.10: 4 residues within 4Å: Chain D: R.57 Chain F: L.46, W.87, V.91 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.46, F:V.91 F09.19: 4 residues within 4Å: Chain G: R.57 Chain I: L.46, W.87, V.91 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:L.46, I:V.91 F09.28: 4 residues within 4Å: Chain J: R.57 Chain L: L.46, W.87, V.91 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:L.46, L:V.91

24 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.2: 15 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.3, K.11, K.12, K.20, K.21, K.29, K.30 Ligand excluded by PLIP K.3: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.2, K.4, K.11, K.12, K.13, K.20, K.21, K.22, K.29, K.30, K.31 Ligand excluded by PLIP K.4: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.5, K.12, K.13, K.14, K.21, K.22, K.23, K.30, K.31, K.32 Ligand excluded by PLIP K.5: 11 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.4, K.13, K.14, K.22, K.23, K.31, K.32 Ligand excluded by PLIP K.6: 7 residues within 4Å: Ligands: K.7, K.15, K.16, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.7: 7 residues within 4Å: Ligands: K.6, K.15, K.16, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.11: 15 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.2, K.3, K.12, K.20, K.21, K.29, K.30 Ligand excluded by PLIP K.12: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.2, K.3, K.4, K.11, K.13, K.20, K.21, K.22, K.29, K.30, K.31 Ligand excluded by PLIP K.13: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.4, K.5, K.12, K.14, K.21, K.22, K.23, K.30, K.31, K.32 Ligand excluded by PLIP K.14: 11 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.4, K.5, K.13, K.22, K.23, K.31, K.32 Ligand excluded by PLIP K.15: 7 residues within 4Å: Ligands: K.6, K.7, K.16, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.16: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.20: 15 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.2, K.3, K.11, K.12, K.21, K.29, K.30 Ligand excluded by PLIP K.21: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.2, K.3, K.4, K.11, K.12, K.13, K.20, K.22, K.29, K.30, K.31 Ligand excluded by PLIP K.22: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.4, K.5, K.12, K.13, K.14, K.21, K.23, K.30, K.31, K.32 Ligand excluded by PLIP K.23: 11 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.4, K.5, K.13, K.14, K.22, K.31, K.32 Ligand excluded by PLIP K.24: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.16, K.25, K.33, K.34 Ligand excluded by PLIP K.25: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.16, K.24, K.33, K.34 Ligand excluded by PLIP K.29: 15 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.2, K.3, K.11, K.12, K.20, K.21, K.30 Ligand excluded by PLIP K.30: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.2, K.3, K.4, K.11, K.12, K.13, K.20, K.21, K.22, K.29, K.31 Ligand excluded by PLIP K.31: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.4, K.5, K.12, K.13, K.14, K.21, K.22, K.23, K.30, K.32 Ligand excluded by PLIP K.32: 11 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.4, K.5, K.13, K.14, K.22, K.23, K.31 Ligand excluded by PLIP K.33: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.16, K.24, K.25, K.34 Ligand excluded by PLIP K.34: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.16, K.24, K.25, K.33 Ligand excluded by PLIP

4 x L2C: (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE(Non-covalent)

L2C.8: 9 residues within 4Å: Chain C: V.84, T.85, L.86, R.89, V.93 Chain H: Y.50, E.53 Chain I: Y.62, P.63 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:L.86, C:V.93 Water bridges: C:L.86, C:R.89, C:R.89 Salt bridges: C:R.89 Hydrogen bonds: H:E.53 L2C.17: 9 residues within 4Å: Chain F: V.84, T.85, L.86, R.89, V.93 Chain K: Y.50, E.53 Chain L: Y.62, P.63 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: F:L.86, F:V.93 Water bridges: F:L.86, F:R.89, F:R.89 Salt bridges: F:R.89 Hydrogen bonds: K:E.53 L2C.26: 9 residues within 4Å: Chain E: Y.50, E.53 Chain F: Y.62, P.63 Chain I: V.84, T.85, L.86, R.89, V.93 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: I:L.86, I:V.93 Water bridges: I:L.86, I:R.89, I:R.89 Salt bridges: I:R.89 Hydrogen bonds: E:E.53 L2C.35: 9 residues within 4Å: Chain B: Y.50, E.53 Chain C: Y.62, P.63 Chain L: V.84, T.85, L.86, R.89, V.93 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain L Hydrogen bonds: B:E.53 Hydrophobic interactions: L:L.86, L:V.93 Water bridges: L:L.86, L:R.89, L:R.89 Salt bridges: L:R.89

4 x TBA: TETRABUTYLAMMONIUM ION(Non-covalent)

TBA.9: 18 residues within 4Å: Chain C: T.74, T.75, I.100, F.103 Chain F: T.74, T.75, F.103 Chain I: A.73, T.74, T.75, I.100, F.103 Chain L: T.74, T.75, I.100 Ligands: TBA.18, TBA.27, TBA.36 9 PLIP interactions: 1 interactions with chain F, 3 interactions with chain I, 3 interactions with chain C, 2 interactions with chain L Hydrophobic interactions: F:F.103, I:I.100, I:F.103, I:F.103, C:I.100, C:I.100, C:F.103, L:T.75, L:I.100 TBA.18: 18 residues within 4Å: Chain C: T.74, T.75, F.103 Chain F: T.74, T.75, I.100, F.103 Chain I: T.74, T.75, I.100 Chain L: A.73, T.74, T.75, I.100, F.103 Ligands: TBA.9, TBA.27, TBA.36 9 PLIP interactions: 3 interactions with chain F, 2 interactions with chain I, 3 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: F:I.100, F:I.100, F:F.103, I:T.75, I:I.100, L:I.100, L:F.103, L:F.103, C:F.103 TBA.27: 18 residues within 4Å: Chain C: T.74, T.75, I.100 Chain F: A.73, T.74, T.75, I.100, F.103 Chain I: T.74, T.75, I.100, F.103 Chain L: T.74, T.75, F.103 Ligands: TBA.9, TBA.18, TBA.36 9 PLIP interactions: 3 interactions with chain F, 3 interactions with chain I, 2 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: F:I.100, F:F.103, F:F.103, I:I.100, I:I.100, I:F.103, C:T.75, C:I.100, L:F.103 TBA.36: 18 residues within 4Å: Chain C: A.73, T.74, T.75, I.100, F.103 Chain F: T.74, T.75, I.100 Chain I: T.74, T.75, F.103 Chain L: T.74, T.75, I.100, F.103 Ligands: TBA.9, TBA.18, TBA.27 9 PLIP interactions: 2 interactions with chain F, 3 interactions with chain C, 3 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: F:T.75, F:I.100, C:I.100, C:F.103, C:F.103, L:I.100, L:I.100, L:F.103, I:F.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yohannan, S. et al., Crystallographic Study of the Tetrabutylammonium Block to the KcsA K(+) Channel. J.Mol.Biol. (2007)

Release Date

2007-02-20

Peptides

Antibody Fab heavy chain: ADGJ
Antibody Fab light chain: BEHK
Voltage-gated potassium channel: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
C

F
C

I
C

L
C

Membrane

We predict this structure to be a membrane protein.
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Antibody Fab heavy chain

Antibody Fab light chain

Voltage-gated potassium channel

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