SMTL ID : 1k4d.1

Potassium Channel KcsA-Fab complex in low concentration of K+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-4-4-4-mer

Ligands

8 x K: POTASSIUM ION(Non-covalent)

K.1: 11 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.6, K.11, K.16 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:G.77, F:G.77, L:G.77, I:G.77 K.2: 7 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.7, K.12, K.17 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F Metal complexes: L:T.75, I:T.75, C:T.75, F:T.75 K.6: 11 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.1, K.11, K.16 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:G.77, F:G.77, L:G.77, I:G.77 K.7: 7 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.2, K.12, K.17 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F Metal complexes: L:T.75, I:T.75, C:T.75, F:T.75 K.11: 11 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.1, K.6, K.16 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:G.77, F:G.77, L:G.77, I:G.77 K.12: 7 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.2, K.7, K.17 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F Metal complexes: L:T.75, I:T.75, C:T.75, F:T.75 K.16: 11 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.1, K.6, K.11 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain L, 1 interactions with chain I, 1 interactions with chain F Metal complexes: C:G.77, L:G.77, I:G.77, F:G.77 K.17: 7 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.2, K.7, K.12 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 1 interactions with chain I, 1 interactions with chain L Metal complexes: F:T.75, C:T.75, I:T.75, L:T.75

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Ligands: NA.8, NA.13, NA.18 No protein-ligand interaction detected (PLIP) NA.8: 3 residues within 4Å: Ligands: NA.3, NA.13, NA.18 No protein-ligand interaction detected (PLIP) NA.13: 3 residues within 4Å: Ligands: NA.3, NA.8, NA.18 No protein-ligand interaction detected (PLIP) NA.18: 3 residues within 4Å: Ligands: NA.3, NA.8, NA.13 No protein-ligand interaction detected (PLIP)

4 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.4: 9 residues within 4Å: Chain C: L.86, R.89, V.93 Chain H: E.53 Chain I: Y.45, Y.62, P.63, L.66, W.67 8 PLIP interactions: 1 interactions with chain H, 4 interactions with chain I, 3 interactions with chain C Hydrogen bonds: H:E.53 Hydrophobic interactions: I:Y.45, I:P.63, I:L.66, I:W.67, C:V.93 Water bridges: C:R.89 Salt bridges: C:R.89 DGA.9: 9 residues within 4Å: Chain F: L.86, R.89, V.93 Chain K: E.53 Chain L: Y.45, Y.62, P.63, L.66, W.67 8 PLIP interactions: 4 interactions with chain L, 1 interactions with chain K, 3 interactions with chain F Hydrophobic interactions: L:Y.45, L:P.63, L:L.66, L:W.67, F:V.93 Hydrogen bonds: K:E.53 Water bridges: F:R.89 Salt bridges: F:R.89 DGA.14: 9 residues within 4Å: Chain E: E.53 Chain F: Y.45, Y.62, P.63, L.66, W.67 Chain I: L.86, R.89, V.93 8 PLIP interactions: 1 interactions with chain E, 3 interactions with chain I, 4 interactions with chain F Hydrogen bonds: E:E.53 Hydrophobic interactions: I:V.93, F:Y.45, F:P.63, F:L.66, F:W.67 Water bridges: I:R.89 Salt bridges: I:R.89 DGA.19: 9 residues within 4Å: Chain B: E.53 Chain C: Y.45, Y.62, P.63, L.66, W.67 Chain L: L.86, R.89, V.93 8 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 3 interactions with chain L Hydrophobic interactions: C:Y.45, C:P.63, C:L.66, C:W.67, L:V.93 Hydrogen bonds: B:E.53 Water bridges: L:R.89 Salt bridges: L:R.89

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

F09.5: 6 residues within 4Å: Chain A: R.57 Chain C: L.49, W.87, C.90, V.91, V.94 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.91, C:V.94 Hydrogen bonds: A:R.57 F09.10: 6 residues within 4Å: Chain D: R.57 Chain F: L.49, W.87, C.90, V.91, V.94 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:V.91, F:V.94 Hydrogen bonds: D:R.57 F09.15: 6 residues within 4Å: Chain G: R.57 Chain I: L.49, W.87, C.90, V.91, V.94 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:V.91, I:V.94 Hydrogen bonds: G:R.57 F09.20: 6 residues within 4Å: Chain J: R.57 Chain L: L.49, W.87, C.90, V.91, V.94 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain L Hydrogen bonds: J:R.57 Hydrophobic interactions: L:V.91, L:V.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution. Nature (2001)

Release Date

2001-11-14

Peptides

antibody Fab fragment heavy chain: ADGJ
antibody Fab fragment light chain: BEHK
potassium channel KcsA: 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 heavy chain

antibody Fab fragment light chain

potassium channel KcsA

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