SMTL ID : 3sya.1

Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with sodium and PIP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: D.179, R.181, S.183, L.226, V.227 Chain C: H.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.179, C:H.20 NA.8: 6 residues within 4Å: Chain B: D.179, R.181, S.183, L.226, V.227 Chain D: H.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.179, B:V.227 NA.15: 6 residues within 4Å: Chain B: H.20 Chain C: D.179, R.181, S.183, L.226, V.227 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.179, C:D.179 NA.22: 6 residues within 4Å: Chain A: H.20 Chain D: D.179, R.181, S.183, L.226, V.227 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.20, D:D.179

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.2: 9 residues within 4Å: Chain A: K.15, L.40, K.41, W.42, R.43, K.145, Q.148, K.150, K.151 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.42, A:R.43, A:Q.148 Salt bridges: A:K.15, A:K.145, A:K.150, A:K.150, A:K.151 PIO.9: 9 residues within 4Å: Chain B: K.15, L.40, K.41, W.42, R.43, K.145, Q.148, K.150, K.151 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.42, B:R.43, B:Q.148 Salt bridges: B:K.15, B:K.145, B:K.150, B:K.150, B:K.151 PIO.16: 9 residues within 4Å: Chain C: K.15, L.40, K.41, W.42, R.43, K.145, Q.148, K.150, K.151 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:W.42, C:R.43, C:Q.148 Salt bridges: C:K.15, C:K.145, C:K.150, C:K.150, C:K.151 PIO.23: 9 residues within 4Å: Chain D: K.15, L.40, K.41, W.42, R.43, K.145, Q.148, K.150, K.151 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:W.42, D:R.43, D:Q.148 Salt bridges: D:K.15, D:K.145, D:K.150, D:K.150, D:K.151

20 x K: POTASSIUM ION(Non-covalent)

K.3: 15 residues within 4Å: Chain A: G.107, Y.108 Chain B: G.107, Y.108 Chain C: G.107, Y.108 Chain D: G.107, Y.108 Ligands: K.4, K.10, K.11, K.17, K.18, K.24, K.25 Ligand excluded by PLIP K.4: 19 residues within 4Å: Chain A: I.106, G.107 Chain B: I.106, G.107 Chain C: I.106, G.107 Chain D: I.106, G.107 Ligands: K.3, K.5, K.10, K.11, K.12, K.17, K.18, K.19, K.24, K.25, K.26 Ligand excluded by PLIP K.5: 19 residues within 4Å: Chain A: T.105, I.106 Chain B: T.105, I.106 Chain C: T.105, I.106 Chain D: T.105, I.106 Ligands: K.4, K.6, K.11, K.12, K.13, K.18, K.19, K.20, K.25, K.26, K.27 Ligand excluded by PLIP K.6: 11 residues within 4Å: Chain A: T.105 Chain B: T.105 Chain C: T.105 Chain D: T.105 Ligands: K.5, K.12, K.13, K.19, K.20, K.26, K.27 Ligand excluded by PLIP K.7: 3 residues within 4Å: Chain A: Y.217 Ligands: K.21, K.28 Ligand excluded by PLIP K.10: 15 residues within 4Å: Chain A: G.107, Y.108 Chain B: G.107, Y.108 Chain C: G.107, Y.108 Chain D: G.107, Y.108 Ligands: K.3, K.4, K.11, K.17, K.18, K.24, K.25 Ligand excluded by PLIP K.11: 19 residues within 4Å: Chain A: I.106, G.107 Chain B: I.106, G.107 Chain C: I.106, G.107 Chain D: I.106, G.107 Ligands: K.3, K.4, K.5, K.10, K.12, K.17, K.18, K.19, K.24, K.25, K.26 Ligand excluded by PLIP K.12: 19 residues within 4Å: Chain A: T.105, I.106 Chain B: T.105, I.106 Chain C: T.105, I.106 Chain D: T.105, I.106 Ligands: K.4, K.5, K.6, K.11, K.13, K.18, K.19, K.20, K.25, K.26, K.27 Ligand excluded by PLIP K.13: 11 residues within 4Å: Chain A: T.105 Chain B: T.105 Chain C: T.105 Chain D: T.105 Ligands: K.5, K.6, K.12, K.19, K.20, K.26, K.27 Ligand excluded by PLIP K.14: 3 residues within 4Å: Chain B: Y.217 Ligands: K.21, K.28 Ligand excluded by PLIP K.17: 15 residues within 4Å: Chain A: G.107, Y.108 Chain B: G.107, Y.108 Chain C: G.107, Y.108 Chain D: G.107, Y.108 Ligands: K.3, K.4, K.10, K.11, K.18, K.24, K.25 Ligand excluded by PLIP K.18: 19 residues within 4Å: Chain A: I.106, G.107 Chain B: I.106, G.107 Chain C: I.106, G.107 Chain D: I.106, G.107 Ligands: K.3, K.4, K.5, K.10, K.11, K.12, K.17, K.19, K.24, K.25, K.26 Ligand excluded by PLIP K.19: 19 residues within 4Å: Chain A: T.105, I.106 Chain B: T.105, I.106 Chain C: T.105, I.106 Chain D: T.105, I.106 Ligands: K.4, K.5, K.6, K.11, K.12, K.13, K.18, K.20, K.25, K.26, K.27 Ligand excluded by PLIP K.20: 11 residues within 4Å: Chain A: T.105 Chain B: T.105 Chain C: T.105 Chain D: T.105 Ligands: K.5, K.6, K.12, K.13, K.19, K.26, K.27 Ligand excluded by PLIP K.21: 3 residues within 4Å: Chain C: Y.217 Ligands: K.7, K.14 Ligand excluded by PLIP K.24: 15 residues within 4Å: Chain A: G.107, Y.108 Chain B: G.107, Y.108 Chain C: G.107, Y.108 Chain D: G.107, Y.108 Ligands: K.3, K.4, K.10, K.11, K.17, K.18, K.25 Ligand excluded by PLIP K.25: 19 residues within 4Å: Chain A: I.106, G.107 Chain B: I.106, G.107 Chain C: I.106, G.107 Chain D: I.106, G.107 Ligands: K.3, K.4, K.5, K.10, K.11, K.12, K.17, K.18, K.19, K.24, K.26 Ligand excluded by PLIP K.26: 19 residues within 4Å: Chain A: T.105, I.106 Chain B: T.105, I.106 Chain C: T.105, I.106 Chain D: T.105, I.106 Ligands: K.4, K.5, K.6, K.11, K.12, K.13, K.18, K.19, K.20, K.25, K.27 Ligand excluded by PLIP K.27: 11 residues within 4Å: Chain A: T.105 Chain B: T.105 Chain C: T.105 Chain D: T.105 Ligands: K.5, K.6, K.12, K.13, K.19, K.20, K.26 Ligand excluded by PLIP K.28: 3 residues within 4Å: Chain D: Y.217 Ligands: K.7, K.14 Ligand excluded by PLIP

Links

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Citation

Whorton, M.R. et al., Crystal Structure of the Mammalian GIRK2 K(+) Channel and Gating Regulation by G Proteins, PIP(2), and Sodium. Cell(Cambridge,Mass.) (2011)

Release Date

2011-10-12

Peptides

G protein-activated inward rectifier potassium channel 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Membrane

We predict this structure to be a membrane protein.
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G protein-activated inward rectifier potassium channel 2

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