8BSU

Crystal structure of the kainate receptor GluK3-H523A ligand binding domain in complex with kainate and the positive allosteric modulator BPAM344 at 2.9A resolution

PDB DOI: https://doi.org/10.2210/pdb8BSU/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-11-26 Released: 2023-12-13
Deposition Author(s): Venskutonyte, R., Frydenvang, K., Kastrup, J.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.234
R-Value Work: 0.207
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Positive allosteric modulation of homomeric kainate receptors GluK1-3

Bay, Y., Venskutonyte, R., Frantsen, S.M., Thorsen, T.S., Musgaard, M., Frydenvang, K., Francotte, P., Pirotte, B., Biggin, P.C., Kristensen, A.S., Boesen, T., Pickering, D.S., Gajhede, M., Kastrup, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 240.08 kDa
Atom Count: 16,506
Modelled Residue Count: 2,000
Deposited Residue Count: 2,064
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 3	A, B, C, D, E A, B, C, D, E, F, G, H	258	Rattus norvegicus	Mutation(s): 1 Gene Names: Grik3, Glur7
UniProt
Find proteins for P42264 (Rattus norvegicus) Explore P42264 Go to UniProtKB: P42264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42264
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2J9 (Subject of Investigation/LOI) Query on 2J9 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain NB [auth F] SDF format, chain OA [auth D] SDF format, chain XA [auth E] SDF format, chain EA [auth C] SDF format, chain T [auth B] SDF format, chain WA [auth E] SDF format, chain WB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth D] MOL2 format, chain XA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain WB [auth G]	EA [auth C] I [auth A] NB [auth F] OA [auth D] T [auth B] EA [auth C], I [auth A], NB [auth F], OA [auth D], T [auth B], WA [auth E], WB [auth G], XA [auth E]	4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide C₁₀ H₁₁ F N₂ O₂ S FLTMTBPCYAZIKM-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain NB [auth F] Focus chain OA [auth D] Focus chain T [auth B] Focus chain WA [auth E] Focus chain WB [auth G] Focus chain XA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain NB [auth F] Focus chain OA [auth D] Focus chain T [auth B] Focus chain WA [auth E] Focus chain WB [auth G] Focus chain XA [auth E]
KAI (Subject of Investigation/LOI) Query on KAI Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain NA [auth C] SDF format, chain DC [auth G] SDF format, chain LC [auth H] SDF format, chain MB [auth E] SDF format, chain R [auth A] SDF format, chain UB [auth F] SDF format, chain VA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain DC [auth G] MOL2 format, chain LC [auth H] MOL2 format, chain MB [auth E] MOL2 format, chain R [auth A] MOL2 format, chain UB [auth F] MOL2 format, chain VA [auth D]	CA [auth B] DC [auth G] LC [auth H] MB [auth E] NA [auth C] CA [auth B], DC [auth G], LC [auth H], MB [auth E], NA [auth C], R [auth A], UB [auth F], VA [auth D]	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE C₁₀ H₁₅ N O₄ VLSMHEGGTFMBBZ-OOZYFLPDSA-N		Interactions Focus chain CA [auth B] Focus chain DC [auth G] Focus chain LC [auth H] Focus chain MB [auth E] Focus chain NA [auth C] Focus chain R [auth A] Focus chain UB [auth F] Focus chain VA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DC [auth G] Focus chain LC [auth H] Focus chain MB [auth E] Focus chain NA [auth C] Focus chain R [auth A] Focus chain UB [auth F] Focus chain VA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain UA [auth D] SDF format, chain BA [auth B] SDF format, chain CC [auth G] SDF format, chain KC [auth H] SDF format, chain LB [auth E] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CC [auth G] MOL2 format, chain KC [auth H] MOL2 format, chain LB [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth D]	BA [auth B] CC [auth G] KC [auth H] LB [auth E] P [auth A] BA [auth B], CC [auth G], KC [auth H], LB [auth E], P [auth A], Q [auth A], TA [auth D], UA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain CC [auth G] Focus chain KC [auth H] Focus chain LB [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CC [auth G] Focus chain KC [auth H] Focus chain LB [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth D] Focus chain UA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GC [auth H] SDF format, chain JB [auth E] SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HA [auth C] SDF format, chain HB [auth E] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain L [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain W [auth B] MOL2 format, chain GC [auth H] MOL2 format, chain JB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain L [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B]	EB [auth E] FB [auth E] GB [auth E] GC [auth H] HA [auth C] EB [auth E], FB [auth E], GB [auth E], GC [auth H], HA [auth C], HB [auth E], IA [auth C], IB [auth E], JB [auth E], L [auth A], RA [auth D], SA [auth D], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain L [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Interactions & Density Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain L [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DB [auth E] SDF format, chain QA [auth D] SDF format, chain XB [auth G] SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain EC [auth H] SDF format, chain FA [auth C] SDF format, chain FC [auth H] SDF format, chain GA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain OB [auth F] SDF format, chain PA [auth D] SDF format, chain PB [auth F] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain YA [auth E] SDF format, chain YB [auth G] SDF format, chain ZA [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain QA [auth D] MOL2 format, chain XB [auth G] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain EC [auth H] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth H] MOL2 format, chain GA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth F] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain YB [auth G] MOL2 format, chain ZA [auth E]	AB [auth E] BB [auth E] CB [auth E] DB [auth E] EC [auth H] AB [auth E], BB [auth E], CB [auth E], DB [auth E], EC [auth H], FA [auth C], FC [auth H], GA [auth C], J [auth A], K [auth A], OB [auth F], PA [auth D], PB [auth F], QA [auth D], U [auth B], V [auth B], XB [auth G], YA [auth E], YB [auth G], ZA [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain OB [auth F] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain XB [auth G] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain OB [auth F] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain XB [auth G] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain ZA [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain S [auth A] SDF format, chain VB [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain VB [auth F]	DA [auth B], S [auth A], VB [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain S [auth A] Focus chain VB [auth F] Interactions & Density Focus chain DA [auth B] Focus chain S [auth A] Focus chain VB [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain IC [auth H] SDF format, chain KA [auth C] SDF format, chain KB [auth E] SDF format, chain N [auth A] SDF format, chain RB [auth F] SDF format, chain TB [auth F] SDF format, chain AA [auth B] SDF format, chain AC [auth G] SDF format, chain BC [auth G] SDF format, chain HC [auth H] SDF format, chain JA [auth C] SDF format, chain JC [auth H] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain O [auth A] SDF format, chain QB [auth F] SDF format, chain SB [auth F] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZB [auth G] MOL2 format, chain IC [auth H] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth E] MOL2 format, chain N [auth A] MOL2 format, chain RB [auth F] MOL2 format, chain TB [auth F] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth G] MOL2 format, chain BC [auth G] MOL2 format, chain HC [auth H] MOL2 format, chain JA [auth C] MOL2 format, chain JC [auth H] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain QB [auth F] MOL2 format, chain SB [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth G]	AA [auth B] AC [auth G] BC [auth G] HC [auth H] IC [auth H] AA [auth B], AC [auth G], BC [auth G], HC [auth H], IC [auth H], JA [auth C], JC [auth H], KA [auth C], KB [auth E], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], QB [auth F], RB [auth F], SB [auth F], TB [auth F], X [auth B], Y [auth B], Z [auth B], ZB [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AC [auth G] Focus chain BC [auth G] Focus chain HC [auth H] Focus chain IC [auth H] Focus chain JA [auth C] Focus chain JC [auth H] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain TB [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth G] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth G] Focus chain BC [auth G] Focus chain HC [auth H] Focus chain IC [auth H] Focus chain JA [auth C] Focus chain JC [auth H] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain TB [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth G]