SMTL ID : 7mit.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

1 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)

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

K.2: 9 residues within 4Å: Chain A: I.141, G.142 Chain B: I.141, G.142 Chain C: I.141, G.142 Chain D: I.141, G.142 Ligands: K.4 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:I.141, A:G.142, D:I.141, C:G.142, B:I.141 K.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.4: 9 residues within 4Å: Chain A: G.142, F.143 Chain B: G.142, F.143 Chain C: G.142, F.143 Chain D: G.142, F.143 Ligands: K.2 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain C Metal complexes: B:G.142, D:F.143, A:G.142, A:F.143, C:F.143 K.19: 4 residues within 4Å: Chain A: T.140 Chain B: T.140 Chain C: T.140 Chain D: T.140 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Metal complexes: B:T.140, C:T.140, A:T.140, D:T.140

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

ATP.5: 11 residues within 4Å: Chain A: I.192, F.193, R.195, Y.339, S.340, F.342, G.343, N.344 Chain D: N.49, I.50, R.51 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:R.51, A:R.195, A:Y.339, A:G.343, A:G.343 Salt bridges: D:R.51 pi-Cation interactions: D:R.51 ATP.10: 10 residues within 4Å: Chain A: N.49, I.50, R.51 Chain B: I.192, F.193, S.194, R.195, L.215, Y.339, G.343 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.49, A:R.51, B:R.195, B:G.343 Salt bridges: A:R.51, A:R.51, B:R.195, B:R.195, B:R.195 pi-Cation interactions: A:R.51 ATP.11: 10 residues within 4Å: Chain B: N.49, I.50, R.51 Chain C: F.193, R.195, Y.339, S.340, F.342, G.343, N.344 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:N.49, B:R.51, B:R.51, B:R.51, C:S.340, C:G.343, C:N.344 pi-Cation interactions: B:R.51 Salt bridges: C:R.195, C:R.195 ATP.14: 11 residues within 4Å: Chain C: N.49, I.50, R.51 Chain D: I.192, F.193, S.194, R.195, L.215, Y.339, F.342, G.343 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.51, D:R.195, D:Y.339, D:G.343 Salt bridges: C:R.51 pi-Cation interactions: C:R.51 ATP.23: 11 residues within 4Å: Chain E: T.397, N.399, W.677, V.703, G.704, C.705, G.706, K.707, S.708, S.709, Q.753 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:T.397, E:N.399, E:N.399, E:G.704, E:G.704, E:C.705, E:G.706, E:K.707, E:S.708, E:S.709, E:Q.753 pi-Stacking: E:W.677, E:W.677, E:W.677

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

POV.6: 11 residues within 4Å: Chain A: W.92, M.105, R.125, S.126, F.127 Chain E: L.3, S.4, F.5, Y.13, L.102 Ligands: POV.22 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:F.127 Hydrogen bonds: A:F.127, E:S.4, E:F.5, E:Y.13 POV.8: 4 residues within 4Å: Chain A: I.156, T.157 Chain B: T.128 Ligands: POV.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.156 POV.12: 8 residues within 4Å: Chain B: L.85, I.89, W.92, M.105, R.125, S.126, F.127 Ligands: POV.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.85, B:I.89, B:W.92, B:F.127, B:F.127 Hydrogen bonds: B:F.127 POV.15: 7 residues within 4Å: Chain C: L.85, I.89, W.92, R.125, F.127, F.131 Ligands: POV.18 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.85, C:I.89, C:W.92, C:F.127, C:F.127, C:F.131, C:F.131 Hydrogen bonds: C:F.127 POV.17: 8 residues within 4Å: Chain C: P.153, I.156, T.157, I.160 Chain D: L.85, F.127, F.131 Ligands: POV.21 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.85, D:L.85, C:I.160 POV.18: 6 residues within 4Å: Chain B: P.153, T.157, I.160 Chain C: T.128 Ligands: POV.15, P5S.16 No protein-ligand interaction detected (PLIP) POV.21: 7 residues within 4Å: Chain D: I.89, W.92, M.105, R.125, S.126, F.127 Ligands: POV.17 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.89, D:F.127 Hydrogen bonds: D:F.127 POV.22: 11 residues within 4Å: Chain A: L.81, L.85, T.128, F.131 Chain D: P.153, T.157, I.160, L.161 Chain E: S.2, L.3 Ligands: POV.6 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.81, A:L.85, A:F.131, A:F.131, D:I.160, D:L.161

8 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.7: 7 residues within 4Å: Chain A: M.90, A.97, H.98, L.154, V.158 Chain E: V.19, F.25 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:F.25, A:A.97, A:L.154, A:L.154, A:V.158 Salt bridges: A:H.98 PTY.25: 11 residues within 4Å: Chain E: W.63, H.123, T.127, V.220, N.221, L.223, S.224, W.229, Y.1221 Ligands: PTY.28, PTY.33 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.223, E:Y.1221 Hydrogen bonds: E:N.221, E:S.224 Salt bridges: E:H.123 PTY.26: 5 residues within 4Å: Chain E: R.295, L.299, T.302 Ligands: P5S.29, P5S.31 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.302 Salt bridges: E:R.295 PTY.27: 7 residues within 4Å: Chain E: I.87, A.88, I.91, S.95, H.349, V.353, I.1232 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.87, E:V.353, E:V.353, E:I.1232 Hydrogen bonds: E:S.95 Salt bridges: E:H.349, E:H.349 PTY.28: 7 residues within 4Å: Chain E: W.229, N.232, I.236, R.1218, L.1222 Ligands: PTY.25, PTY.33 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:R.1218, E:L.1222 Hydrogen bonds: E:N.232 PTY.30: 8 residues within 4Å: Chain A: T.63, L.67, H.71 Chain E: L.45, F.46, I.47, T.117, N.124 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:L.45, E:L.45, E:F.46, E:T.117 Salt bridges: A:H.71, A:H.71 PTY.32: 10 residues within 4Å: Chain E: F.81, A.313, L.316, C.317, L.351, L.354, L.357, A.358, L.361 Ligands: P5S.29 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.81, E:F.81, E:A.313, E:L.351, E:L.354, E:A.358, E:L.361 PTY.33: 9 residues within 4Å: Chain E: W.73, L.80, T.116, V.120, H.123, N.124, L.223 Ligands: PTY.25, PTY.28 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:W.73, E:L.80, E:T.116, E:V.120, E:L.223 Salt bridges: E:H.123, E:H.123

6 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.9: 11 residues within 4Å: Chain A: K.68, W.69, R.70, V.74, T.77, M.78 Chain D: Q.58, L.64, S.79, L.86, V.172 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.69, A:W.69, A:W.69, A:V.74, A:T.77, D:L.64, D:L.86, D:V.172 Hydrogen bonds: A:W.69, A:R.70, D:Q.58 Salt bridges: A:R.70 P5S.13: 10 residues within 4Å: Chain A: Q.58, S.79, I.160, L.161, I.164 Chain B: K.68, W.69, R.70, V.74, T.77 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:I.160, A:L.161, A:I.164, B:W.69, B:R.70, B:R.70, B:V.74, B:T.77 Hydrogen bonds: A:Q.58, B:W.69 Salt bridges: B:K.68, B:R.70, B:R.70 P5S.16: 12 residues within 4Å: Chain B: Q.58, F.61, L.64, S.79, C.82, L.161, I.164 Chain C: K.68, W.69, R.70, T.77 Ligands: POV.18 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.69, C:W.69, C:T.77, B:L.64, B:L.161, B:I.164 Hydrogen bonds: C:W.69, C:R.70, B:Q.58 Salt bridges: C:K.68 P5S.20: 13 residues within 4Å: Chain C: L.57, Q.58, F.61, S.83, L.86, I.168, I.169, V.172 Chain D: K.68, W.69, R.70, L.73, V.74 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:F.61, C:L.86, C:I.168, C:I.168, C:I.169, C:V.172, C:V.172, D:W.69, D:W.69, D:L.73, D:V.74 Hydrogen bonds: C:Q.58, D:W.69, D:R.70 Salt bridges: D:R.70 P5S.29: 17 residues within 4Å: Chain E: F.77, A.78, F.81, Q.217, P.218, K.225, A.226, L.299, F.303, L.310, F.365, A.368, Y.371, V.372 Ligands: PTY.26, P5S.31, PTY.32 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.77, E:A.78, E:F.81, E:A.226, E:F.303, E:L.310, E:F.365, E:A.368 Hydrogen bonds: E:Q.217, E:P.218 Salt bridges: E:K.225 P5S.31: 14 residues within 4Å: Chain E: H.65, P.67, H.69, N.70, L.71, A.78, V.82, G.178, L.179, A.182, N.186, K.225 Ligands: PTY.26, P5S.29 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:N.70, E:L.71, E:A.78, E:V.82, E:L.179, E:N.186 Hydrogen bonds: E:P.67, E:H.69, E:N.70, E:N.70, E:K.225

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

GBM.24: 14 residues within 4Å: Chain A: M.1, L.2, R.4 Chain E: R.304, Y.370, I.374, L.427, N.430, L.584, Y.1205, L.1208, N.1212, R.1213, R.1263 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.374, E:L.584, E:Y.1205, E:L.1208 Hydrogen bonds: E:R.304, E:N.430, E:N.1212, E:R.1213, E:R.1213, E:R.1263, E:R.1263, A:L.2

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: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

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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