SMTL ID : 2jk5.1

Potassium Channel KcsA in complex with Tetrabutylammonium in high K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.1: 7 residues within 4Å: Chain C: H.124 Chain F: H.124 Chain I: H.124 Chain L: H.124 Ligands: CO.12, CO.23, CO.34 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain L Metal complexes: F:H.124, I:H.124, C:H.124, L:H.124 CO.12: 7 residues within 4Å: Chain C: H.124 Chain F: H.124 Chain I: H.124 Chain L: H.124 Ligands: CO.1, CO.23, CO.34 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain L Metal complexes: F:H.124, I:H.124, C:H.124, L:H.124 CO.23: 7 residues within 4Å: Chain C: H.124 Chain F: H.124 Chain I: H.124 Chain L: H.124 Ligands: CO.1, CO.12, CO.34 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain L Metal complexes: F:H.124, I:H.124, C:H.124, L:H.124 CO.34: 7 residues within 4Å: Chain C: H.124 Chain F: H.124 Chain I: H.124 Chain L: H.124 Ligands: CO.1, CO.12, CO.23 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain L, 1 interactions with chain C, 1 interactions with chain I Metal complexes: F:H.124, L:H.124, C:H.124, I:H.124

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

K.2: 19 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.6, K.13, K.14, K.17, K.24, K.25, K.28, K.35, K.36, K.39 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.13, K.14, K.15, K.24, K.25, K.26, K.35, K.36, K.37 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.14, K.15, K.16, K.25, K.26, K.27, K.36, K.37, K.38 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.15, K.16, K.26, K.27, K.37, K.38 Ligand excluded by PLIP K.6: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.2, K.7, K.13, K.17, K.18, K.24, K.28, K.29, K.35, K.39, K.40 Ligand excluded by PLIP K.7: 7 residues within 4Å: Ligands: K.6, K.17, K.18, K.28, K.29, K.39, K.40 Ligand excluded by PLIP K.13: 19 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.6, K.14, K.17, K.24, K.25, K.28, K.35, K.36, K.39 Ligand excluded by PLIP K.14: 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.13, K.15, K.24, K.25, K.26, K.35, K.36, K.37 Ligand excluded by PLIP K.15: 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.14, K.16, K.25, K.26, K.27, K.36, K.37, K.38 Ligand excluded by PLIP K.16: 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.15, K.26, K.27, K.37, K.38 Ligand excluded by PLIP K.17: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.2, K.6, K.7, K.13, K.18, K.24, K.28, K.29, K.35, K.39, K.40 Ligand excluded by PLIP K.18: 7 residues within 4Å: Ligands: K.6, K.7, K.17, K.28, K.29, K.39, K.40 Ligand excluded by PLIP K.24: 19 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.6, K.13, K.14, K.17, K.25, K.28, K.35, K.36, K.39 Ligand excluded by PLIP K.25: 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.13, K.14, K.15, K.24, K.26, K.35, K.36, K.37 Ligand excluded by PLIP K.26: 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.14, K.15, K.16, K.25, K.27, K.36, K.37, K.38 Ligand excluded by PLIP K.27: 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.15, K.16, K.26, K.37, K.38 Ligand excluded by PLIP K.28: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.2, K.6, K.7, K.13, K.17, K.18, K.24, K.29, K.35, K.39, K.40 Ligand excluded by PLIP K.29: 7 residues within 4Å: Ligands: K.6, K.7, K.17, K.18, K.28, K.39, K.40 Ligand excluded by PLIP K.35: 19 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.6, K.13, K.14, K.17, K.24, K.25, K.28, K.36, K.39 Ligand excluded by PLIP K.36: 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.13, K.14, K.15, K.24, K.25, K.26, K.35, K.37 Ligand excluded by PLIP K.37: 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.14, K.15, K.16, K.25, K.26, K.27, K.36, K.38 Ligand excluded by PLIP K.38: 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.15, K.16, K.26, K.27, K.37 Ligand excluded by PLIP K.39: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.2, K.6, K.7, K.13, K.17, K.18, K.24, K.28, K.29, K.35, K.40 Ligand excluded by PLIP K.40: 7 residues within 4Å: Ligands: K.6, K.7, K.17, K.18, K.28, K.29, K.39 Ligand excluded by PLIP

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

F09.8: 7 residues within 4Å: Chain C: L.46, L.49, W.87, C.90, V.91, V.94 Ligands: HP6.11 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.46, C:W.87, C:V.91, C:V.94 F09.19: 7 residues within 4Å: Chain F: L.46, L.49, W.87, C.90, V.91, V.94 Ligands: HP6.22 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.46, F:W.87, F:V.91, F:V.94 F09.30: 7 residues within 4Å: Chain I: L.46, L.49, W.87, C.90, V.91, V.94 Ligands: HP6.33 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:L.46, I:W.87, I:V.91, I:V.94 F09.41: 7 residues within 4Å: Chain L: L.46, L.49, W.87, C.90, V.91, V.94 Ligands: HP6.44 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:L.46, L:W.87, L:V.91, L:V.94

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

L2C.9: 9 residues within 4Å: Chain C: V.84, T.85, L.86, R.89 Chain E: E.53 Chain F: L.41, P.63, L.66, W.67 7 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: F:P.63, F:L.66, F:W.67, C:L.86 Water bridges: C:R.89 Salt bridges: C:R.89 Hydrogen bonds: E:E.53 L2C.20: 9 residues within 4Å: Chain F: V.84, T.85, L.86, R.89 Chain K: E.53 Chain L: L.41, P.63, L.66, W.67 7 PLIP interactions: 3 interactions with chain L, 3 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: L:P.63, L:L.66, L:W.67, F:L.86 Water bridges: F:R.89 Salt bridges: F:R.89 Hydrogen bonds: K:E.53 L2C.31: 9 residues within 4Å: Chain B: E.53 Chain C: L.41, P.63, L.66, W.67 Chain I: V.84, T.85, L.86, R.89 7 PLIP interactions: 3 interactions with chain I, 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: I:L.86, C:P.63, C:L.66, C:W.67 Water bridges: I:R.89 Salt bridges: I:R.89 Hydrogen bonds: B:E.53 L2C.42: 9 residues within 4Å: Chain H: E.53 Chain I: L.41, P.63, L.66, W.67 Chain L: V.84, T.85, L.86, R.89 7 PLIP interactions: 1 interactions with chain H, 3 interactions with chain I, 3 interactions with chain L Hydrogen bonds: H:E.53 Hydrophobic interactions: I:P.63, I:L.66, I:W.67, L:L.86 Water bridges: L:R.89 Salt bridges: L:R.89

4 x TBA: TETRABUTYLAMMONIUM ION(Non-covalent)

TBA.10: 20 residues within 4Å: Chain C: A.73, T.74, T.75, I.100 Chain F: A.73, T.74, T.75, I.100, F.103 Chain I: A.73, T.74, T.75, I.100 Chain L: A.73, T.74, T.75, I.100 Ligands: TBA.21, TBA.32, TBA.43 12 PLIP interactions: 3 interactions with chain I, 4 interactions with chain F, 2 interactions with chain L, 3 interactions with chain C Hydrophobic interactions: I:T.75, I:I.100, I:I.100, F:T.75, F:I.100, F:I.100, F:F.103, L:T.75, L:I.100, C:T.75, C:I.100, C:I.100 TBA.21: 20 residues within 4Å: Chain C: A.73, T.74, T.75, I.100 Chain F: A.73, T.74, T.75, I.100 Chain I: A.73, T.74, T.75, I.100 Chain L: A.73, T.74, T.75, I.100, F.103 Ligands: TBA.10, TBA.32, TBA.43 12 PLIP interactions: 2 interactions with chain I, 3 interactions with chain F, 4 interactions with chain L, 3 interactions with chain C Hydrophobic interactions: I:T.75, I:I.100, F:T.75, F:I.100, F:I.100, L:T.75, L:I.100, L:I.100, L:F.103, C:T.75, C:I.100, C:I.100 TBA.32: 20 residues within 4Å: Chain C: A.73, T.74, T.75, I.100, F.103 Chain F: A.73, T.74, T.75, I.100 Chain I: A.73, T.74, T.75, I.100 Chain L: A.73, T.74, T.75, I.100 Ligands: TBA.10, TBA.21, TBA.43 12 PLIP interactions: 3 interactions with chain I, 2 interactions with chain F, 3 interactions with chain L, 4 interactions with chain C Hydrophobic interactions: I:T.75, I:I.100, I:I.100, F:T.75, F:I.100, L:T.75, L:I.100, L:I.100, C:T.75, C:I.100, C:I.100, C:F.103 TBA.43: 20 residues within 4Å: Chain C: A.73, T.74, T.75, I.100 Chain F: A.73, T.74, T.75, I.100 Chain I: A.73, T.74, T.75, I.100, F.103 Chain L: A.73, T.74, T.75, I.100 Ligands: TBA.10, TBA.21, TBA.32 12 PLIP interactions: 4 interactions with chain I, 2 interactions with chain C, 3 interactions with chain L, 3 interactions with chain F Hydrophobic interactions: I:T.75, I:I.100, I:I.100, I:F.103, C:T.75, C:I.100, L:T.75, L:I.100, L:I.100, F:T.75, F:I.100, F:I.100

4 x HP6: HEPTANE(Non-covalent)

HP6.11: 5 residues within 4Å: Chain C: V.39, G.43, L.46, V.94 Ligands: F09.8 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.39, C:L.46, C:V.94 HP6.22: 5 residues within 4Å: Chain F: V.39, G.43, L.46, V.94 Ligands: F09.19 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:V.39, F:L.46, F:V.94 HP6.33: 5 residues within 4Å: Chain I: V.39, G.43, L.46, V.94 Ligands: F09.30 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:V.39, I:L.46, I:V.94 HP6.44: 5 residues within 4Å: Chain L: V.39, G.43, L.46, V.94 Ligands: F09.41 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:V.39, L:L.46, L:V.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenaeus, M.J. et al., Structures of Kcsa in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site. Biochemistry (2014)

Release Date

2009-11-17

Peptides

ANTIBODY FAB FRAGMENT LIGHT CHAIN: ADGJ
ANTIBODY FAB FRAGMENT HEAVY 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 FRAGMENT LIGHT CHAIN

ANTIBODY FAB FRAGMENT HEAVY CHAIN

VOLTAGE-GATED POTASSIUM CHANNEL

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