SMTL ID : 7mjo.1

Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain E: N.9, S.11 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain F: N.9 No protein-ligand interaction detected (PLIP)

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

K.3: 4 residues within 4Å: Chain A: T.140 Chain B: T.140 Chain C: T.140 Chain D: T.140 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 interactions with chain A Metal complexes: D:T.140, D:T.140, C:T.140, A:T.140, A:T.140 K.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 8 residues within 4Å: Chain A: I.192, F.193, R.195, Y.339, G.343 Chain D: N.49, I.50, R.51 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:N.49, D:R.51, D:R.51, D:R.51, A:G.343 Salt bridges: A:R.195, A:R.195, A:R.195 ATP.10: 10 residues within 4Å: Chain A: N.49, I.50, R.51 Chain B: I.192, F.193, R.195, L.215, Y.339, F.342, G.343 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.49, A:R.51, A:R.51, B:R.195, B:G.343 Salt bridges: B:R.195, B:R.195 ATP.11: 7 residues within 4Å: Chain B: N.49, I.50, R.51 Chain C: I.192, F.193, R.195, G.343 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.49, B:R.51, C:R.195, C:G.343 Salt bridges: B:R.51, C:R.195 ATP.13: 6 residues within 4Å: Chain C: I.50, R.51 Chain D: I.192, R.195, F.342, G.343 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.49, C:R.51, C:R.51, D:R.195, D:R.195, D:G.343, D:G.343 pi-Stacking: D:F.342 ATP.19: 8 residues within 4Å: Chain E: W.677, Q.702, C.705, G.706, K.707, S.708, S.709, Q.753 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:C.705, E:G.706, E:K.707, E:S.708, E:S.709, E:Q.753 Salt bridges: E:K.707, E:K.707 pi-Stacking: E:W.677

10 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.6: 7 residues within 4Å: Chain A: L.57, Q.58, F.61 Chain B: W.69, R.70, V.74 Ligands: PTY.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.57, A:F.61, B:V.74 PTY.7: 4 residues within 4Å: Chain A: F.56, L.57 Chain E: K.132 Ligands: PTY.6 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Salt bridges: E:K.132, E:K.132 Hydrogen bonds: A:L.57 PTY.8: 6 residues within 4Å: Chain A: W.69, R.70 Chain D: Q.58, I.60, F.61, M.173 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.69, D:I.60, D:F.61 PTY.9: 11 residues within 4Å: Chain A: W.92, M.105, R.125, S.126, F.127, T.128 Chain D: T.157 Chain E: L.3, S.4, F.5 Ligands: PTY.18 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:F.127, E:F.5 PTY.14: 7 residues within 4Å: Chain B: F.56, L.57, Q.58 Chain C: K.68, W.69, R.70, L.73 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.69, C:L.73 Hydrogen bonds: C:R.70, B:Q.58 PTY.15: 5 residues within 4Å: Chain C: L.57, Q.58 Chain D: W.69, R.70, R.187 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.69, D:W.69 Hydrogen bonds: D:W.69, D:R.70, D:R.187 Salt bridges: D:R.70 PTY.18: 4 residues within 4Å: Chain D: E.151 Chain E: S.2, L.3 Ligands: PTY.9 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.3 PTY.21: 3 residues within 4Å: Chain E: R.100, E.327, K.329 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:R.100 Hydrogen bonds: E:K.329 Salt bridges: E:R.100 PTY.22: 4 residues within 4Å: Chain A: M.90, A.97, L.154 Chain E: V.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.97, A:L.154 PTY.23: 8 residues within 4Å: Chain A: L.67 Chain E: F.42, L.45, F.46, I.47, G.48, V.120, N.124 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.42, E:F.42, E:F.46, E:F.46, E:V.120

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.12: 5 residues within 4Å: Chain B: W.92, M.105, R.125, S.126, F.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.127 POV.16: 4 residues within 4Å: Chain C: L.85, W.92, I.101, R.125 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.85 POV.17: 9 residues within 4Å: Chain D: W.92, M.105, R.125, S.126, F.127, T.128 Chain F: L.3, S.4, F.5 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.127 Hydrogen bonds: D:F.127

1 x GBM: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide(Non-covalent)

GBM.20: 12 residues within 4Å: Chain E: Y.370, W.423, F.426, L.427, N.430, L.584, Y.1205, L.1208, S.1209, N.1212, R.1213, R.1263 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.370, E:W.423, E:F.426, E:Y.1205, E:L.1208 Hydrogen bonds: E:N.430, E:R.1213, E:R.1213, E:R.1263, E:R.1263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sung, M.W. et al., Vascular K ATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-10-13

Peptides

ATP-sensitive inward rectifier potassium channel 8: ABCD
Isoform SUR2B of ATP-binding cassette sub-family C member 9: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

Membrane

We predict this structure to be a membrane protein.
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ATP-sensitive inward rectifier potassium channel 8

Isoform SUR2B of ATP-binding cassette sub-family C member 9

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