7LDE

native AMPA receptor

PDB DOI: https://doi.org/10.2210/pdb7LDE/pdb
EM Map EMD-23284: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli, Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2021-01-13 Released: 2021-05-12
Deposition Author(s): Yu, J., Rao, P., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 698.34 kDa
Atom Count: 34,424
Modelled Residue Count: 4,990
Deposited Residue Count: 6,234
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 1	A, C	907	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23818 (Mus musculus) Explore P23818 Go to UniProtKB: P23818
IMPC: MGI:95808
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23818
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor	B, D	883	Mus musculus	Mutation(s): 1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23819 (Mus musculus) Explore P23819 Go to UniProtKB: P23819
IMPC: MGI:95809
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23819
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cornichon homolog 2	E, F	160	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O35089 (Mus musculus) Explore O35089 Go to UniProtKB: O35089
IMPC: MGI:1277225
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35089
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel gamma-8 subunit	G, H	423	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8VHW2 (Mus musculus) Explore Q8VHW2 Go to UniProtKB: Q8VHW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VHW2
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
11B8 scFv	I, L	257	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
15F1 Fab light chain	J, M	225	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
15F1 Fab heavy chain	K, N	262	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, P, Q, R, S	2		N-Glycosylation	Interactions Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Interactions & Density Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZK1 Query on ZK1 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain IA [auth C] SDF format, chain T [auth A] SDF format, chain WA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain WA [auth D]	BA [auth B], IA [auth C], T [auth A], WA [auth D]	{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid C₁₄ H₁₅ F₃ N₃ O₆ P WZMQMKNCWDCCMT-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain IA [auth C] Focus chain T [auth A] Focus chain WA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain IA [auth C] Focus chain T [auth A] Focus chain WA [auth D]
XVD (Subject of Investigation/LOI) Query on XVD Download Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain LB [auth H] MOL2 format, chain FB [auth G] MOL2 format, chain LB [auth H]	FB [auth G], LB [auth H]	6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol C₁₄ H₈ Cl F₃ N₂ O₂ COBXSLRIXGQVGS-UHFFFAOYSA-N		Interactions Focus chain FB [auth G] Focus chain LB [auth H] Interactions & Density Focus chain FB [auth G] Focus chain LB [auth H]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain U [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain U [auth A]	JA [auth C], U [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain JA [auth C] Focus chain U [auth A] Interactions & Density Focus chain JA [auth C] Focus chain U [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	CA [auth B] NA [auth C] OA [auth C] PA [auth C] XA [auth D] CA [auth B], NA [auth C], OA [auth C], PA [auth C], XA [auth D], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth B] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth B] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain Z [auth A]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain EA [auth B] SDF format, chain HB [auth G] SDF format, chain NB [auth H] SDF format, chain SA [auth D] SDF format, chain ZA [auth E] MOL2 format, chain BB [auth F] MOL2 format, chain EA [auth B] MOL2 format, chain HB [auth G] MOL2 format, chain NB [auth H] MOL2 format, chain SA [auth D] MOL2 format, chain ZA [auth E]	BB [auth F] EA [auth B] HB [auth G] NB [auth H] SA [auth D] BB [auth F], EA [auth B], HB [auth G], NB [auth H], SA [auth D], ZA [auth E]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain EA [auth B] Focus chain HB [auth G] Focus chain NB [auth H] Focus chain SA [auth D] Focus chain ZA [auth E] Interactions & Density Focus chain BB [auth F] Focus chain EA [auth B] Focus chain HB [auth G] Focus chain NB [auth H] Focus chain SA [auth D] Focus chain ZA [auth E]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain DB [auth G] SDF format, chain EB [auth G] SDF format, chain IB [auth H] SDF format, chain JB [auth H] SDF format, chain RA [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain IB [auth H] MOL2 format, chain JB [auth H] MOL2 format, chain RA [auth D]	DA [auth B] DB [auth G] EB [auth G] IB [auth H] JB [auth H] DA [auth B], DB [auth G], EB [auth G], IB [auth H], JB [auth H], RA [auth D]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain RA [auth D] Interactions & Density Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain RA [auth D]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain CB [auth G] SDF format, chain KB [auth H] SDF format, chain MA [auth C] SDF format, chain X [auth A] SDF format, chain YA [auth E] MOL2 format, chain AB [auth F] MOL2 format, chain CB [auth G] MOL2 format, chain KB [auth H] MOL2 format, chain MA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth E]	AB [auth F] CB [auth G] KB [auth H] MA [auth C] X [auth A] AB [auth F], CB [auth G], KB [auth H], MA [auth C], X [auth A], YA [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain CB [auth G] Focus chain KB [auth H] Focus chain MA [auth C] Focus chain X [auth A] Focus chain YA [auth E] Interactions & Density Focus chain AB [auth F] Focus chain CB [auth G] Focus chain KB [auth H] Focus chain MA [auth C] Focus chain X [auth A] Focus chain YA [auth E]
DD9 Query on DD9 Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain TA [auth D] SDF format, chain VA [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D]	FA [auth B], HA [auth B], TA [auth D], VA [auth D]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain HA [auth B] Focus chain TA [auth D] Focus chain VA [auth D] Interactions & Density Focus chain FA [auth B] Focus chain HA [auth B] Focus chain TA [auth D] Focus chain VA [auth D]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain GB [auth G] SDF format, chain KA [auth C] SDF format, chain MB [auth H] SDF format, chain UA [auth D] SDF format, chain V [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth G] MOL2 format, chain KA [auth C] MOL2 format, chain MB [auth H] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth A]	GA [auth B] GB [auth G] KA [auth C] MB [auth H] UA [auth D] GA [auth B], GB [auth G], KA [auth C], MB [auth H], UA [auth D], V [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain GB [auth G] Focus chain KA [auth C] Focus chain MB [auth H] Focus chain UA [auth D] Focus chain V [auth A] Interactions & Density Focus chain GA [auth B] Focus chain GB [auth G] Focus chain KA [auth C] Focus chain MB [auth H] Focus chain UA [auth D] Focus chain V [auth A]
HP6 Query on HP6 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain LA [auth C] SDF format, chain QA [auth C] SDF format, chain W [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain W [auth A]	AA [auth A], LA [auth C], QA [auth C], W [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain LA [auth C] Focus chain QA [auth C] Focus chain W [auth A] Interactions & Density Focus chain AA [auth A] Focus chain LA [auth C] Focus chain QA [auth C] Focus chain W [auth A]