8VRN

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus PPTQ

PDB DOI: https://doi.org/10.2210/pdb8VRN/pdb
EM Map EMD-43485: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Homo sapiens, Spodoptera
Mutation(s): No

Deposited: 2024-01-22 Released: 2024-06-26
Deposition Author(s): Chojnacka, W., Teng, J., Kim, J.J., Jensen, A.A., Hibbs, R.E.
Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.57 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus methaqualone

Chojnacka, W., Hibbs, R.E., Teng, J., Kim, J.J., Jensen, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 372.57 kDa
Atom Count: 17,865
Modelled Residue Count: 2,121
Deposited Residue Count: 3,195
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-2	A, C	364	Homo sapiens	Mutation(s): 0 Gene Names: GABRB2
UniProt & NIH Common Fund Data Resources
Find proteins for P47870 (Homo sapiens) Explore P47870 Go to UniProtKB: P47870
PHAROS: P47870 GTEx: ENSG00000145864
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47870
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-1	B, D	358	Homo sapiens	Mutation(s): 0 Gene Names: GABRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens) Explore P14867 Go to UniProtKB: P14867
PHAROS: P14867 GTEx: ENSG00000022355
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14867
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit gamma-2	E	417	Homo sapiens	Mutation(s): 0 Gene Names: GABRG2
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens) Explore P18507 Go to UniProtKB: P18507
PHAROS: P18507 GTEx: ENSG00000113327
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18507
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa FAB light chain	F [auth I], H [auth L]	213	Mus musculus	Mutation(s): 0 Gene Names: LC
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG2B FAB heavy chain	G [auth J], I [auth K]	454	Mus musculus	Mutation(s): 0 Gene Names: Ighg
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F], N, O	2		N-Glycosylation	Interactions Focus chain J [auth F] Focus chain N Focus chain O Interactions & Density Focus chain J [auth F] Focus chain N Focus chain O

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	K [auth G], M, P	5		N-Glycosylation	Interactions Focus chain K [auth G] Focus chain M Focus chain P Interactions & Density Focus chain K [auth G] Focus chain M Focus chain P

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	L [auth H]	10		N-Glycosylation	Interactions Focus chain L [auth H] Interactions & Density Focus chain L [auth H]

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q3G Query on Q3G Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain Y [auth C]	AA [auth D], Y [auth C]	O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine C₄₀ H₇₈ N O₁₀ P WZFUPCSEUKNOBF-PQQNNWGCSA-N		Interactions Focus chain AA [auth D] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain Y [auth C]
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B]	U [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth B] SDF format, chain Z [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth C]	BA [auth D], S [auth A], T [auth B], X [auth C], Z [auth C]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain BA [auth D] Focus chain S [auth A] Focus chain T [auth B] Focus chain X [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain S [auth A] Focus chain T [auth B] Focus chain X [auth C] Focus chain Z [auth C]
A1ADN (Subject of Investigation/LOI) Query on A1ADN Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain W [auth C] MOL2 format, chain R [auth A] MOL2 format, chain W [auth C]	R [auth A], W [auth C]	3-(4-methylphenyl)-2-phenylquinazolin-4(3H)-one C₂₁ H₁₆ N₂ O QBGIEWLTLCNRED-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain W [auth C] Interactions & Density Focus chain R [auth A] Focus chain W [auth C]
ABU Query on ABU Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain V [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth C]	Q [auth A], V [auth C]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain V [auth C] Interactions & Density Focus chain Q [auth A] Focus chain V [auth C]