- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-1-1-1-2-mer
- Ligands
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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
- 2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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
- 2 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.8: 15 residues within 4Å:- Chain A: R.240, E.294, T.297, F.301, K.303, R.304, K.317, N.378, S.379, S.381, K.382, I.383, L.386, S.387
- Ligands: D10.11
19 PLIP interactions:19 interactions with chain A- Hydrophobic interactions: A:E.294, A:T.297, A:L.386, A:L.386
- Hydrogen bonds: A:R.240, A:R.240, A:N.378, A:S.379, A:K.382, A:K.382, A:K.382
- Salt bridges: A:R.240, A:K.303, A:K.303, A:R.304, A:K.317, A:K.317, A:K.382, A:K.382
PIO.34: 15 residues within 4Å:- Chain D: R.240, I.293, F.301, K.303, R.304, K.317, F.377, N.378, S.379, S.381, K.382, I.383, L.386
- Ligands: HEX.35, HEX.37
14 PLIP interactions:14 interactions with chain D- Hydrophobic interactions: D:I.293, D:L.386
- Hydrogen bonds: D:R.240, D:S.379, D:S.379, D:K.382
- Salt bridges: D:R.240, D:K.303, D:K.303, D:R.304, D:K.317, D:K.317, D:K.382, D:K.382
- 5 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)
PGW.9: 13 residues within 4Å:- Chain A: K.213, I.214, G.215, L.223, I.226, I.230, P.392, F.395, N.399, W.403, L.407
- Chain B: P.270
- Ligands: PX2.17
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:I.226, A:I.230, A:P.392, A:F.395, A:N.399, A:W.403, A:W.403
- Hydrogen bonds: A:G.215
PGW.36: 17 residues within 4Å:- Chain D: K.213, I.214, G.215, V.218, L.223, P.224, I.226, P.392, F.395, N.399, W.403
- Chain E: M.280, F.283, V.284
- Ligands: D10.39, PX2.42, R16.48
13 PLIP interactions:11 interactions with chain D, 2 interactions with chain E- Hydrophobic interactions: D:I.214, D:V.218, D:L.223, D:P.224, D:I.226, D:P.392, D:N.399, D:W.403, D:W.403, E:F.283, E:V.284
- Hydrogen bonds: D:I.214, D:G.215
PGW.45: 5 residues within 4Å:- Chain A: A.272
- Chain E: N.211, I.212, G.213
- Ligands: R16.43
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:I.212, E:G.213
PGW.52: 21 residues within 4Å:- Chain B: N.211, I.212, G.213, I.216, L.217, L.225
- Chain C: S.256, S.267, Y.268, V.269, L.274, S.277, F.280, I.281
- Chain G: F.71, T.72, D.73, F.74, S.75
- Ligands: D10.24, CLR.32
13 PLIP interactions:3 interactions with chain C, 5 interactions with chain B, 5 interactions with chain G- Hydrophobic interactions: C:L.274, C:F.280, B:I.216, B:L.217, B:L.217, G:F.74
- Hydrogen bonds: C:S.267, B:I.212, B:G.213, G:D.73, G:D.73, G:F.74, G:S.75
PGW.54: 13 residues within 4Å:- Chain C: T.388, L.395
- Chain G: R.10, A.17, I.18, I.21, I.100, F.103, F.106, F.107, F.108, Y.115
- Ligands: D10.53
12 PLIP interactions:10 interactions with chain G, 2 interactions with chain C- Hydrophobic interactions: G:A.17, G:I.21, G:F.103, G:F.106, G:F.106, G:F.107, G:F.107, G:F.107, C:T.388, C:L.395
- Hydrogen bonds: G:F.107
- Salt bridges: G:R.10
- 12 x D10: DECANE(Non-covalent)
D10.10: 5 residues within 4Å:- Chain A: A.282, Y.285, A.286, F.289
- Chain E: L.225
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain E- Hydrophobic interactions: A:Y.285, A:A.286, A:F.289, E:L.225
D10.11: 4 residues within 4Å:- Chain A: I.293
- Ligands: PIO.8, D10.15, PLM.47
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:I.293
D10.12: 3 residues within 4Å:- Chain A: L.400, W.403, L.407
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.400, A:W.403, A:L.407
D10.15: 4 residues within 4Å:- Chain A: Y.300
- Ligands: D10.11, PLM.47, HEX.50
No protein-ligand interaction detected (PLIP)D10.19: 4 residues within 4Å:- Chain B: S.430, L.434, W.437
- Ligands: R16.18
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.434, B:W.437
D10.24: 3 residues within 4Å:- Chain B: I.216
- Ligands: R16.18, PGW.52
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:I.216
D10.27: 2 residues within 4Å:- Chain C: F.296, H.372
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:F.296
D10.38: 6 residues within 4Å:- Chain C: I.218, L.222
- Chain D: A.282, A.286, F.289
- Ligands: PX2.40
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain D- Hydrophobic interactions: C:I.218, D:A.286, D:F.289
D10.39: 5 residues within 4Å:- Chain D: G.396, L.400, L.407
- Ligands: PGW.36, PX2.42
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:L.407
D10.44: 2 residues within 4Å:- Chain E: W.437
- Ligands: R16.43
No protein-ligand interaction detected (PLIP)D10.49: 6 residues within 4Å:- Chain E: M.277, F.432, V.435, Y.439, Y.440
- Ligands: R16.48
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:F.432, E:V.435, E:Y.439
D10.53: 7 residues within 4Å:- Chain C: L.392, L.395, V.396, V.399
- Chain G: I.25, L.97
- Ligands: PGW.54
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain G- Hydrophobic interactions: C:L.392, C:L.395, C:V.396, C:V.399, G:L.97
- 5 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)
PX2.13: 11 residues within 4Å:- Chain A: W.279, V.283, A.286, F.287, S.290, L.394, F.398, V.401, Y.402, T.405, Y.406
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:V.283, A:V.283, A:A.286, A:F.287, A:F.287, A:F.287, A:F.287, A:L.394, A:F.398, A:V.401, A:Y.402, A:T.405
PX2.17: 9 residues within 4Å:- Chain A: V.234, W.237, R.388, P.392
- Chain B: L.291, F.295, Y.298, R.303
- Ligands: PGW.9
7 PLIP interactions:3 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:L.291, B:F.295, A:V.234, A:W.237, A:W.237, A:W.237
- Salt bridges: B:R.303
PX2.26: 8 residues within 4Å:- Chain C: S.380, R.383, I.384, P.387
- Chain D: Y.300
- Chain G: F.108
- Ligands: PLM.29, PLM.31
5 PLIP interactions:3 interactions with chain C, 1 interactions with chain D, 1 interactions with chain G- Hydrophobic interactions: C:R.383, C:I.384, C:P.387, G:F.108
- Hydrogen bonds: D:Y.300
PX2.40: 13 residues within 4Å:- Chain D: W.279, A.282, V.283, A.286, F.287, L.394, I.397, F.398, V.401, Y.402, Y.406
- Ligands: HEX.35, D10.38
11 PLIP interactions:11 interactions with chain D- Hydrophobic interactions: D:A.282, D:V.283, D:A.286, D:F.287, D:L.394, D:L.394, D:F.398, D:F.398, D:F.398, D:V.401, D:Y.402
PX2.42: 10 residues within 4Å:- Chain D: V.234, W.237, R.388, P.392, G.396
- Chain E: F.295, Y.298, R.303
- Ligands: PGW.36, D10.39
7 PLIP interactions:5 interactions with chain D, 2 interactions with chain E- Hydrophobic interactions: D:V.234, D:W.237, D:W.237, D:W.237, D:P.392, E:Y.298
- Hydrogen bonds: E:R.303
- 2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)
ABU.14: 10 residues within 4Å:- Chain A: R.58, L.109, T.121
- Chain B: Y.91, E.149, S.150, Y.151, F.194, T.196, Y.199
9 PLIP interactions:7 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:Y.151, B:F.194, B:Y.199, A:L.109
- Hydrogen bonds: B:Y.91, B:S.150, B:Y.151, B:T.196
- Salt bridges: A:R.58
ABU.51: 11 residues within 4Å:- Chain D: F.56, R.58, L.109, T.121
- Chain E: Y.91, E.149, S.150, Y.151, F.194, T.196, Y.199
7 PLIP interactions:5 interactions with chain E, 2 interactions with chain D- Hydrophobic interactions: E:Y.151, E:Y.199, D:L.109
- Hydrogen bonds: E:Y.91, E:S.150, E:Y.199
- Salt bridges: D:R.58
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.16: 6 residues within 4Å:- Chain A: P.43, V.44, L.179, N.180, Q.181, Y.182
Ligand excluded by PLIPCL.33: 5 residues within 4Å:- Chain C: P.40, V.41, L.174, Y.175, Q.176
Ligand excluded by PLIPCL.41: 5 residues within 4Å:- Chain D: V.44, L.179, N.180, Q.181, Y.182
Ligand excluded by PLIPCL.55: 5 residues within 4Å:- Chain G: F.52, S.70, F.71, T.72
- Ligands: CLR.32
Ligand excluded by PLIP- 4 x R16: HEXADECANE(Non-covalent)
R16.18: 7 residues within 4Å:- Chain B: I.224, W.231, S.430, W.437, V.441
- Ligands: D10.19, D10.24
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:W.231, B:W.437, B:V.441
R16.22: 6 residues within 4Å:- Chain B: M.277, L.431, F.432, V.435, Y.436, Y.439
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:L.431, B:F.432, B:F.432, B:V.435, B:Y.439, B:Y.439
R16.43: 7 residues within 4Å:- Chain E: I.216, W.231, F.429, N.433, W.437
- Ligands: D10.44, PGW.45
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:W.231, E:F.429, E:W.437
R16.48: 7 residues within 4Å:- Chain E: V.272, M.277, G.281, V.284, F.432
- Ligands: PGW.36, D10.49
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:V.272, E:V.284, E:F.432
- 7 x HEX: HEXANE(Non-covalent)
HEX.20: 1 residues within 4Å:- Chain B: E.292
No protein-ligand interaction detected (PLIP)HEX.21: 4 residues within 4Å:- Chain B: W.235, I.423, P.426
- Ligands: PLM.30
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:W.235, B:I.423, B:P.426
HEX.23: 5 residues within 4Å:- Chain B: M.277, M.280, G.281, V.284, F.285
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:M.280, B:V.284, B:F.285
HEX.35: 6 residues within 4Å:- Chain D: F.287, S.290, F.391, L.394
- Ligands: PIO.34, PX2.40
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:F.287, D:F.391, D:F.391
HEX.37: 3 residues within 4Å:- Chain D: S.290, E.294
- Ligands: PIO.34
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:E.294, D:E.294
HEX.46: 1 residues within 4Å:- Chain E: E.292
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:E.292
HEX.50: 3 residues within 4Å:- Chain E: I.423, P.426
- Ligands: D10.15
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:I.423, E:P.426
- 5 x PLM: PALMITIC ACID(Non-covalent)
PLM.25: 7 residues within 4Å:- Chain C: C.361, R.374, Y.381
- Chain G: L.105, C.109, N.110, T.113
6 PLIP interactions:4 interactions with chain G, 2 interactions with chain C- Hydrophobic interactions: G:L.105, G:T.113, C:Y.381
- Hydrogen bonds: G:N.110, G:T.113
- Salt bridges: C:R.374
PLM.29: 6 residues within 4Å:- Chain C: F.390, N.394, W.398, L.402
- Ligands: PX2.26, OLC.28
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:F.390, C:W.398, C:W.398
PLM.30: 8 residues within 4Å:- Chain B: W.231, V.232, W.235
- Chain C: T.292, Y.295, F.296, R.300
- Ligands: HEX.21
9 PLIP interactions:5 interactions with chain B, 4 interactions with chain C- Hydrophobic interactions: B:W.231, B:V.232, B:W.235, B:W.235, B:W.235, C:Y.295, C:Y.295, C:F.296
- Salt bridges: C:R.300
PLM.31: 6 residues within 4Å:- Chain C: W.228, V.229, W.232
- Chain D: T.297, Y.300
- Ligands: PX2.26
7 PLIP interactions:2 interactions with chain D, 5 interactions with chain C- Hydrophobic interactions: D:Y.300, D:Y.300, C:W.228, C:V.229, C:W.232, C:W.232, C:W.232
PLM.47: 7 residues within 4Å:- Chain A: I.293, T.297, Y.300, F.301
- Chain E: W.235
- Ligands: D10.11, D10.15
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain E- Hydrophobic interactions: A:I.293, A:Y.300, E:W.235, E:W.235, E:W.235
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 1 x CLR: CHOLESTEROL(Non-covalent)
CLR.32: 16 residues within 4Å:- Chain C: L.274, C.361, F.393, V.396, S.400, Y.401
- Chain G: I.32, F.52, F.71, T.72, L.90, L.97, G.98, T.101
- Ligands: PGW.52, CL.55
11 PLIP interactions:5 interactions with chain G, 6 interactions with chain C- Hydrophobic interactions: G:I.32, G:F.71, G:T.72, G:L.90, G:L.97, C:L.274, C:L.274, C:F.393, C:V.396, C:V.396, C:Y.401
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kasaragod, V.B. et al., CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38, in a desensitised state (StateD1). To Be Published
- Release Date
- 2025-07-02
- Peptides
- Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2: C
Neuroligin-2: F
LHFPL tetraspan subfamily member 4 protein: G
Megabody38: HI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
HG
LH
GI
P - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-1-1-1-2-mer
- Ligands
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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
- 2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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
- 2 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)
- 5 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)
- 12 x D10: DECANE(Non-covalent)
- 5 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)
- 2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x R16: HEXADECANE(Non-covalent)
- 7 x HEX: HEXANE(Non-covalent)
- 5 x PLM: PALMITIC ACID(Non-covalent)
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 1 x CLR: CHOLESTEROL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kasaragod, V.B. et al., CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38, in a desensitised state (StateD1). To Be Published
- Release Date
- 2025-07-02
- Peptides
- Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2: C
Neuroligin-2: F
LHFPL tetraspan subfamily member 4 protein: G
Megabody38: HI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
HG
LH
GI
P - Membrane
-
We predict this structure to be a membrane protein.