SMTL ID : 2dwe.1

Crystal structure of KcsA-FAB-TBA complex in Rb+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-4-4-mer

Ligands

12 x RB: RUBIDIUM ION(Non-covalent)

RB.1: 11 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: RB.7, RB.13, RB.19 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain C Metal complexes: I:Y.57, L:Y.57, F:Y.57, C:Y.57 RB.2: 15 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: RB.3, TBA.6, RB.8, RB.9, TBA.12, RB.14, RB.15, TBA.18, RB.20, RB.21, TBA.24 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain F, 1 interactions with chain C Metal complexes: L:T.54, I:T.54, F:T.54, C:T.54 RB.3: 15 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: RB.2, RB.8, RB.9, RB.14, RB.15, RB.20, RB.21 No protein-ligand interaction detected (PLIP) RB.7: 11 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: RB.1, RB.13, RB.19 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain C Metal complexes: I:Y.57, L:Y.57, F:Y.57, C:Y.57 RB.8: 15 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: RB.2, RB.3, TBA.6, RB.9, TBA.12, RB.14, RB.15, TBA.18, RB.20, RB.21, TBA.24 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain F, 1 interactions with chain C Metal complexes: L:T.54, I:T.54, F:T.54, C:T.54 RB.9: 15 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: RB.2, RB.3, RB.8, RB.14, RB.15, RB.20, RB.21 No protein-ligand interaction detected (PLIP) RB.13: 11 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: RB.1, RB.7, RB.19 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain C Metal complexes: I:Y.57, L:Y.57, F:Y.57, C:Y.57 RB.14: 15 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: RB.2, RB.3, TBA.6, RB.8, RB.9, TBA.12, RB.15, TBA.18, RB.20, RB.21, TBA.24 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain F, 1 interactions with chain C Metal complexes: L:T.54, I:T.54, F:T.54, C:T.54 RB.15: 15 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: RB.2, RB.3, RB.8, RB.9, RB.14, RB.20, RB.21 No protein-ligand interaction detected (PLIP) RB.19: 11 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: RB.1, RB.7, RB.13 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain I, 1 interactions with chain C Metal complexes: L:Y.57, F:Y.57, I:Y.57, C:Y.57 RB.20: 15 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: RB.2, RB.3, TBA.6, RB.8, RB.9, TBA.12, RB.14, RB.15, TBA.18, RB.21, TBA.24 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 interactions with chain L, 1 interactions with chain I Metal complexes: C:T.54, F:T.54, L:T.54, I:T.54 RB.21: 15 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: RB.2, RB.3, RB.8, RB.9, RB.14, RB.15, RB.20 No protein-ligand interaction detected (PLIP)

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

L2C.4: 12 residues within 4Å: Chain C: V.63, T.64, L.65, R.68, V.72 Chain H: E.53 Chain I: L.20, S.23, Y.41, P.42, L.45, V.49 7 PLIP interactions: 3 interactions with chain C, 1 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: C:R.68, C:V.72, I:L.45, I:L.45, I:V.49 Salt bridges: C:R.68 Hydrogen bonds: H:E.53 L2C.10: 12 residues within 4Å: Chain F: V.63, T.64, L.65, R.68, V.72 Chain K: E.53 Chain L: L.20, S.23, Y.41, P.42, L.45, V.49 7 PLIP interactions: 3 interactions with chain L, 3 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: L:L.45, L:L.45, L:V.49, F:R.68, F:V.72 Salt bridges: F:R.68 Hydrogen bonds: K:E.53 L2C.16: 12 residues within 4Å: Chain E: E.53 Chain F: L.20, S.23, Y.41, P.42, L.45, V.49 Chain I: V.63, T.64, L.65, R.68, V.72 7 PLIP interactions: 3 interactions with chain I, 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: I:R.68, I:V.72, F:L.45, F:L.45, F:V.49 Salt bridges: I:R.68 Hydrogen bonds: E:E.53 L2C.22: 12 residues within 4Å: Chain B: E.53 Chain C: L.20, S.23, Y.41, P.42, L.45, V.49 Chain L: V.63, T.64, L.65, R.68, V.72 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain L, 1 interactions with chain B Hydrophobic interactions: C:L.45, C:L.45, C:V.49, L:R.68, L:V.72 Salt bridges: L:R.68 Hydrogen bonds: B:E.53

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

F09.5: 4 residues within 4Å: Chain A: Y.55, R.57 Chain C: W.66, V.70 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.66, C:W.66, C:V.70 Hydrogen bonds: A:R.57 F09.11: 4 residues within 4Å: Chain D: Y.55, R.57 Chain F: W.66, V.70 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:W.66, F:W.66, F:V.70 Hydrogen bonds: D:R.57 F09.17: 4 residues within 4Å: Chain G: Y.55, R.57 Chain I: W.66, V.70 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain I Hydrogen bonds: G:R.57 Hydrophobic interactions: I:W.66, I:W.66, I:V.70 F09.23: 4 residues within 4Å: Chain J: Y.55, R.57 Chain L: W.66, V.70 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: L:W.66, L:W.66, L:V.70 Hydrogen bonds: J:R.57

4 x TBA: TETRABUTYLAMMONIUM ION(Non-covalent)

TBA.6: 24 residues within 4Å: Chain C: A.52, T.53, T.54, I.79, F.82 Chain F: A.52, T.53, T.54, F.82 Chain I: A.52, T.53, T.54, I.79 Chain L: A.52, T.53, T.54, I.79 Ligands: RB.2, RB.8, TBA.12, RB.14, TBA.18, RB.20, TBA.24 8 PLIP interactions: 2 interactions with chain L, 3 interactions with chain C, 2 interactions with chain F, 1 interactions with chain I Hydrophobic interactions: L:T.54, L:I.79, C:T.54, C:I.79, C:F.82, F:T.54, F:F.82, I:I.79 TBA.12: 24 residues within 4Å: Chain C: A.52, T.53, T.54, F.82 Chain F: A.52, T.53, T.54, I.79, F.82 Chain I: A.52, T.53, T.54, I.79 Chain L: A.52, T.53, T.54, I.79 Ligands: RB.2, TBA.6, RB.8, RB.14, TBA.18, RB.20, TBA.24 8 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C, 2 interactions with chain I, 1 interactions with chain L Hydrophobic interactions: F:T.54, F:I.79, F:F.82, C:T.54, C:F.82, I:T.54, I:I.79, L:I.79 TBA.18: 24 residues within 4Å: Chain C: A.52, T.53, T.54, I.79 Chain F: A.52, T.53, T.54, I.79 Chain I: A.52, T.53, T.54, I.79, F.82 Chain L: A.52, T.53, T.54, F.82 Ligands: RB.2, TBA.6, RB.8, TBA.12, RB.14, RB.20, TBA.24 8 PLIP interactions: 3 interactions with chain I, 1 interactions with chain F, 2 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: I:T.54, I:I.79, I:F.82, F:I.79, L:T.54, L:F.82, C:T.54, C:I.79 TBA.24: 24 residues within 4Å: Chain C: A.52, T.53, T.54, I.79 Chain F: A.52, T.53, T.54, I.79 Chain I: A.52, T.53, T.54, F.82 Chain L: A.52, T.53, T.54, I.79, F.82 Ligands: RB.2, TBA.6, RB.8, TBA.12, RB.14, TBA.18, RB.20 8 PLIP interactions: 2 interactions with chain I, 2 interactions with chain F, 3 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: I:T.54, I:F.82, F:T.54, F:I.79, L:T.54, L:I.79, L:F.82, C:I.79

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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