SMTL ID : 5vkh.1

Closed conformation of KcsA Y82A-F103A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-4-4-4-mer

Ligands

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

F09.1: 5 residues within 4Å: Chain A: R.57 Chain C: L.28, A.29, W.66, V.70 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.28, C:A.29, C:W.66, C:W.66 Hydrogen bonds: A:R.57 Water bridges: A:R.57 F09.9: 5 residues within 4Å: Chain D: R.57 Chain F: L.28, A.29, W.66, V.70 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:R.57 Water bridges: D:R.57 Hydrophobic interactions: F:L.28, F:A.29, F:W.66, F:W.66 F09.17: 5 residues within 4Å: Chain G: R.57 Chain I: L.28, A.29, W.66, V.70 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain I Hydrogen bonds: G:R.57 Water bridges: G:R.57 Hydrophobic interactions: I:L.28, I:A.29, I:W.66, I:W.66 F09.25: 5 residues within 4Å: Chain J: R.57 Chain L: L.28, A.29, W.66, V.70 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:L.28, L:A.29, L:W.66, L:W.66 Hydrogen bonds: J:R.57 Water bridges: J:R.57

4 x 1EM: (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE(Non-covalent)

1EM.2: 7 residues within 4Å: Chain C: V.63, L.65, R.68 Chain I: Y.41, P.42, W.46, V.49 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain I Hydrophobic interactions: C:L.65, I:W.46 Hydrogen bonds: C:V.63, C:L.65 Salt bridges: C:R.68 1EM.10: 7 residues within 4Å: Chain F: V.63, L.65, R.68 Chain L: Y.41, P.42, W.46, V.49 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain L Hydrophobic interactions: F:L.65, L:W.46 Hydrogen bonds: F:V.63, F:L.65 Salt bridges: F:R.68 1EM.18: 7 residues within 4Å: Chain F: Y.41, P.42, W.46, V.49 Chain I: V.63, L.65, R.68 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain I Hydrophobic interactions: F:W.46, I:L.65 Hydrogen bonds: I:V.63, I:L.65 Salt bridges: I:R.68 1EM.26: 7 residues within 4Å: Chain C: Y.41, P.42, W.46, V.49 Chain L: V.63, L.65, R.68 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:L.65, C:W.46 Hydrogen bonds: L:V.63, L:L.65 Salt bridges: L:R.68

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

K.3: 15 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: K.4, K.11, K.12, K.19, K.20, K.27, K.28 Ligand excluded by PLIP K.4: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.3, K.5, K.11, K.12, K.13, K.19, K.20, K.21, K.27, K.28, K.29 Ligand excluded by PLIP K.5: 19 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: K.4, K.6, K.12, K.13, K.14, K.20, K.21, K.22, K.28, K.29, K.30 Ligand excluded by PLIP K.6: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.5, K.13, K.14, K.21, K.22, K.29, K.30 Ligand excluded by PLIP K.7: 3 residues within 4Å: Ligands: K.15, K.23, K.31 Ligand excluded by PLIP K.8: 3 residues within 4Å: Ligands: K.16, K.24, K.32 Ligand excluded by PLIP K.11: 15 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: K.3, K.4, K.12, K.19, K.20, K.27, K.28 Ligand excluded by PLIP K.12: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.3, K.4, K.5, K.11, K.13, K.19, K.20, K.21, K.27, K.28, K.29 Ligand excluded by PLIP K.13: 19 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: K.4, K.5, K.6, K.12, K.14, K.20, K.21, K.22, K.28, K.29, K.30 Ligand excluded by PLIP K.14: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.5, K.6, K.13, K.21, K.22, K.29, K.30 Ligand excluded by PLIP K.15: 3 residues within 4Å: Ligands: K.7, K.23, K.31 Ligand excluded by PLIP K.16: 3 residues within 4Å: Ligands: K.8, K.24, K.32 Ligand excluded by PLIP K.19: 15 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: K.3, K.4, K.11, K.12, K.20, K.27, K.28 Ligand excluded by PLIP K.20: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.3, K.4, K.5, K.11, K.12, K.13, K.19, K.21, K.27, K.28, K.29 Ligand excluded by PLIP K.21: 19 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: K.4, K.5, K.6, K.12, K.13, K.14, K.20, K.22, K.28, K.29, K.30 Ligand excluded by PLIP K.22: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.5, K.6, K.13, K.14, K.21, K.29, K.30 Ligand excluded by PLIP K.23: 3 residues within 4Å: Ligands: K.7, K.15, K.31 Ligand excluded by PLIP K.24: 3 residues within 4Å: Ligands: K.8, K.16, K.32 Ligand excluded by PLIP K.27: 15 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: K.3, K.4, K.11, K.12, K.19, K.20, K.28 Ligand excluded by PLIP K.28: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.3, K.4, K.5, K.11, K.12, K.13, K.19, K.20, K.21, K.27, K.29 Ligand excluded by PLIP K.29: 19 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: K.4, K.5, K.6, K.12, K.13, K.14, K.20, K.21, K.22, K.28, K.30 Ligand excluded by PLIP K.30: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.5, K.6, K.13, K.14, K.21, K.22, K.29 Ligand excluded by PLIP K.31: 3 residues within 4Å: Ligands: K.7, K.15, K.23 Ligand excluded by PLIP K.32: 3 residues within 4Å: Ligands: K.8, K.16, K.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuello, L.G. et al., The gating cycle of a K+ channel at atomic resolution. Elife (2017)

Release Date

2017-12-06

Peptides

Antibody Heavy Chain: ADGJ
Antibody Light Chain: BEHK
pH-gated 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 Heavy Chain

Antibody Light Chain

pH-gated potassium channel KcsA

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