SMTL ID : 8pvb.1

Structure of GABAAR determined by cryoEM at 100 keV

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-mer

Ligands

5 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: 4 residues within 4Å: Chain A: P.133, L.134, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: P.133, L.134, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: P.133, L.134, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain G: P.133, L.134, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 4 residues within 4Å: Chain I: P.133, L.134, N.135, H.174 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 13 residues within 4Å: Chain A: N.204, R.247, V.249, S.250, R.251, S.266, R.268 Chain B: N.417, Y.418, G.487, S.490, T.497, D.500 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.247, A:R.251, B:Y.418, B:D.500, A:N.252, B:T.497, B:T.497 NAG-NAG-BMA-MAN-MAN.13: 13 residues within 4Å: Chain C: N.204, R.247, V.249, S.250, R.251, S.266, R.268 Chain D: N.417, Y.418, G.487, S.490, T.497, D.500 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.247, C:R.251, D:Y.418, D:D.500, C:N.252, D:T.497, D:T.497 NAG-NAG-BMA-MAN-MAN.24: 13 residues within 4Å: Chain E: N.204, R.247, V.249, S.250, R.251, S.266, R.268 Chain F: N.417, Y.418, G.487, S.490, T.497, D.500 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Y.418, F:D.500, E:R.247, E:R.251, F:T.497, F:T.497, E:N.252 NAG-NAG-BMA-MAN-MAN.35: 13 residues within 4Å: Chain G: N.204, R.247, V.249, S.250, R.251, S.266, R.268 Chain H: N.417, Y.418, G.487, S.490, T.497, D.500 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.247, G:R.251, H:Y.418, H:D.500, G:N.252, H:T.497, H:T.497 NAG-NAG-BMA-MAN-MAN.46: 13 residues within 4Å: Chain I: N.204, R.247, V.249, S.250, R.251, S.266, R.268 Chain J: N.417, Y.418, G.487, S.490, T.497, D.500 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Y.418, J:D.500, I:R.247, I:R.251, J:T.497, J:T.497, I:N.252

5 x R16: HEXADECANE(Non-covalent)

R16.3: 8 residues within 4Å: Chain A: I.285, W.292, P.380, F.383, S.384, N.387, W.391 Ligands: D10.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.285, A:I.285, A:W.292, A:P.380, A:F.383, A:W.391, A:W.391, A:W.391 R16.14: 8 residues within 4Å: Chain C: I.285, W.292, P.380, F.383, S.384, N.387, W.391 Ligands: D10.17 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.285, C:I.285, C:W.292, C:P.380, C:F.383, C:W.391, C:W.391, C:W.391 R16.25: 8 residues within 4Å: Chain E: I.285, W.292, P.380, F.383, S.384, N.387, W.391 Ligands: D10.28 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.285, E:I.285, E:W.292, E:P.380, E:F.383, E:W.391, E:W.391, E:W.391 R16.36: 8 residues within 4Å: Chain G: I.285, W.292, P.380, F.383, S.384, N.387, W.391 Ligands: D10.39 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:I.285, G:I.285, G:W.292, G:P.380, G:F.383, G:W.391, G:W.391, G:W.391 R16.47: 8 residues within 4Å: Chain I: I.285, W.292, P.380, F.383, S.384, N.387, W.391 Ligands: D10.50 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:I.285, I:I.285, I:W.292, I:P.380, I:F.383, I:W.391, I:W.391, I:W.391

20 x D10: DECANE(Non-covalent)

D10.4: 6 residues within 4Å: Chain A: I.289, V.293, W.296 Chain I: F.356, Y.359 Ligands: D10.5 Ligand excluded by PLIP D10.5: 2 residues within 4Å: Chain A: R.376 Ligands: D10.4 Ligand excluded by PLIP D10.6: 4 residues within 4Å: Chain A: S.384, N.387, W.391 Ligands: R16.3 Ligand excluded by PLIP D10.7: 4 residues within 4Å: Chain A: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.15: 6 residues within 4Å: Chain A: F.356, Y.359 Chain C: I.289, V.293, W.296 Ligands: D10.16 Ligand excluded by PLIP D10.16: 2 residues within 4Å: Chain C: R.376 Ligands: D10.15 Ligand excluded by PLIP D10.17: 4 residues within 4Å: Chain C: S.384, N.387, W.391 Ligands: R16.14 Ligand excluded by PLIP D10.18: 4 residues within 4Å: Chain C: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.26: 6 residues within 4Å: Chain C: F.356, Y.359 Chain E: I.289, V.293, W.296 Ligands: D10.27 Ligand excluded by PLIP D10.27: 2 residues within 4Å: Chain E: R.376 Ligands: D10.26 Ligand excluded by PLIP D10.28: 4 residues within 4Å: Chain E: S.384, N.387, W.391 Ligands: R16.25 Ligand excluded by PLIP D10.29: 4 residues within 4Å: Chain E: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.37: 6 residues within 4Å: Chain E: F.356, Y.359 Chain G: I.289, V.293, W.296 Ligands: D10.38 Ligand excluded by PLIP D10.38: 2 residues within 4Å: Chain G: R.376 Ligands: D10.37 Ligand excluded by PLIP D10.39: 4 residues within 4Å: Chain G: S.384, N.387, W.391 Ligands: R16.36 Ligand excluded by PLIP D10.40: 4 residues within 4Å: Chain G: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.48: 6 residues within 4Å: Chain G: F.356, Y.359 Chain I: I.289, V.293, W.296 Ligands: D10.49 Ligand excluded by PLIP D10.49: 2 residues within 4Å: Chain I: R.376 Ligands: D10.48 Ligand excluded by PLIP D10.50: 4 residues within 4Å: Chain I: S.384, N.387, W.391 Ligands: R16.47 Ligand excluded by PLIP D10.51: 4 residues within 4Å: Chain I: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP

5 x HSM: HISTAMINE(Non-covalent)

HSM.8: 8 residues within 4Å: Chain A: Y.152, E.210, S.211, Y.212, F.255, Y.260 Chain C: D.98, Y.117 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Y.152, A:E.210, A:T.257, C:D.98, C:D.98 Hydrophobic interactions: C:Y.117 pi-Stacking: C:Y.117 HSM.19: 8 residues within 4Å: Chain C: Y.152, E.210, S.211, Y.212, F.255, Y.260 Chain E: D.98, Y.117 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:Y.152, C:E.210, C:T.257, E:D.98, E:D.98 Hydrophobic interactions: E:Y.117 pi-Stacking: E:Y.117 HSM.30: 8 residues within 4Å: Chain E: Y.152, E.210, S.211, Y.212, F.255, Y.260 Chain G: D.98, Y.117 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain G Hydrogen bonds: E:Y.152, E:E.210, E:T.257, G:D.98, G:D.98 Hydrophobic interactions: G:Y.117 pi-Stacking: G:Y.117 HSM.41: 8 residues within 4Å: Chain G: Y.152, E.210, S.211, Y.212, F.255, Y.260 Chain I: D.98, Y.117 7 PLIP interactions: 4 interactions with chain I, 3 interactions with chain G Hydrophobic interactions: I:Y.117 Hydrogen bonds: I:D.98, I:D.98, G:Y.152, G:E.210, G:T.257 pi-Stacking: I:Y.117 HSM.52: 8 residues within 4Å: Chain A: D.98, Y.117 Chain I: Y.152, E.210, S.211, Y.212, F.255, Y.260 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain I Hydrophobic interactions: A:Y.117 Hydrogen bonds: A:D.98, A:D.98, I:Y.152, I:E.210, I:T.257 pi-Stacking: A:Y.117

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Ligands: CL.20, CL.31, CL.42, CL.53 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: H.162, G.163 Chain I: D.156, S.159 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Ligands: CL.9, CL.31, CL.42, CL.53 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: D.156, S.159 Chain C: H.162, G.163 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Ligands: CL.9, CL.20, CL.42, CL.53 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain C: D.156, S.159 Chain E: H.162, G.163 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Ligands: CL.9, CL.20, CL.31, CL.53 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain E: D.156, S.159 Chain G: H.162, G.163 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Ligands: CL.9, CL.20, CL.31, CL.42 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain G: D.156, S.159 Chain I: H.162, G.163 Ligand excluded by PLIP

5 x V8D: Etomidate(Non-covalent)

V8D.11: 12 residues within 4Å: Chain A: M.316, N.320, D.337, L.340, M.341, F.344, V.345 Chain C: L.278, Q.279, M.282, P.283, L.286 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.340, A:F.344, A:V.345, C:L.278, C:L.286 pi-Stacking: A:F.344 V8D.22: 12 residues within 4Å: Chain C: M.316, N.320, D.337, L.340, M.341, F.344, V.345 Chain E: L.278, Q.279, M.282, P.283, L.286 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain C Hydrophobic interactions: E:L.278, E:L.286, C:L.340, C:F.344, C:V.345 pi-Stacking: C:F.344 V8D.33: 12 residues within 4Å: Chain E: M.316, N.320, D.337, L.340, M.341, F.344, V.345 Chain G: L.278, Q.279, M.282, P.283, L.286 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: E:L.340, E:F.344, E:V.345, G:L.278, G:L.286 pi-Stacking: E:F.344 V8D.44: 12 residues within 4Å: Chain G: M.316, N.320, D.337, L.340, M.341, F.344, V.345 Chain I: L.278, Q.279, M.282, P.283, L.286 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain I Hydrophobic interactions: G:L.340, G:F.344, G:V.345, I:L.278, I:L.286 pi-Stacking: G:F.344 V8D.55: 12 residues within 4Å: Chain A: L.278, Q.279, M.282, P.283, L.286 Chain I: M.316, N.320, D.337, L.340, M.341, F.344, V.345 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:L.340, I:F.344, I:V.345, A:L.278, A:L.286 pi-Stacking: I:F.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McMullan, G. et al., Structure determination by cryoEM at 100 keV. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-11-29

Peptides

Gamma-aminobutyric acid receptor subunit beta-3: ACEGI
Megabody Mb25: BDFHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

B
O

D
O

F
O

H
O

J
O

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-3

Megabody Mb25

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