9GIB: NMDA

NMDA bound to compound 380. Determined by X-ray diffraction at 1.95 Å resolution. Released 27 Nov 2024.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 2
Atoms: 4,744
Mol. weight: 65.86 kDa
Ligands: GLU, A1ILP
Released: 27 Nov 2024

Explore 9GIB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GIB contains 32 α-helices and 41 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	405-410	6	1
β-strand	413	1	2
β-strand	417	1	2
β-strand	418-421	4	1
α-helix	422-423	2
β-strand	434-441	8	1
β-strand	449-457	9	1
α-helix	459-471	13
β-strand	474-479	6	1
β-strand	488-489	2	3
β-strand	492-493	2	3
α-helix	495-501	7
β-strand	507-508	2	1
β-strand	513	1	4
α-helix	516-519	4
β-strand	522-524	3	1
β-strand	529-538	10	4
α-helix	668-671	4
α-helix	673-675	3
α-helix	679-680	2
β-strand	682-683	2	4
α-helix	689-697	9
α-helix	699-705	7
α-helix	706-708	3
α-helix	713-721	9
β-strand	727-731	5	4
α-helix	732-740	9
α-helix	743-745	3
β-strand	747-749	3	4
β-strand	756-761	6	4
β-strand	764-766	3	1
α-helix	772-784	13
α-helix	787-795	9

Chain B: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	398-402	5	5
β-strand	405	1	6
β-strand	409	1	6
β-strand	410-413	4	5
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	7
β-strand	430	1	7
α-helix	431-432	2
β-strand	434-439	6	5
β-strand	450-456	7	5
α-helix	458-470	13
β-strand	474-478	5	5
β-strand	487-489	3	8
β-strand	496-498	3	8
α-helix	500-506	7
β-strand	512-513	2	5
α-helix	517	1
β-strand	518	1	9
α-helix	519	1
α-helix	521-524	4
β-strand	528-529	2	5
α-helix	530	1
α-helix	532	1
β-strand	534-543	10	9
β-strand	544	1	10
β-strand	546	1	10
α-helix	670-673	4
β-strand	681-682	2	9
β-strand	684	1	11
α-helix	690-695	6
α-helix	700-707	8
β-strand	711	1	11
α-helix	714-722	9
β-strand	728-732	5	9
α-helix	733-742	10
β-strand	746-758	13	9
β-strand	761-762	2	5
α-helix	769-781	13
α-helix	784-792	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor	A	protein	285	Rattus norvegicus	Q00959 (AlphaFold model)
Isoform 1 of Glutamate receptor ionotropic, NMDA 1	B	protein	291	Homo sapiens	Q05586 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GIB_1 Glutamate receptor (chains A)
GSPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKG
FCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEER
SEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNN
YPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFA
TTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHN

Sequence of entity 2 (B), FASTA

>9GIB_2 Isoform 1 of Glutamate receptor ionotropic, NMDA 1 (chains B)
MSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQ
CCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMI
VAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSV
DIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTT
GELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	1
A1ILP	(2~{R})-2-azanyl-3-[[3-(5-ethyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylami…	C15 H16 F N3 O4	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Advancements in NMDA Receptor-Targeted Antidepressants: From d-Cycloserine Discovery to Preclinical Efficacy of Lu AF90103. Ascic, E., Marigo, M., David, L. et al. J Med Chem (2024) 67:20135-20155. DOI 10.1021/acs.jmedchem.4c01477 · PubMed

Other PDB entries of the same protein (UniProt Q00959 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JWX 1.5 Å, GluN2A ligand-binding core in complex with propyl-NHP5G
5U8C 1.6 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…
9GJ1 1.62 Å, NMDA bound to compound 339
6UZ6 1.66 Å, Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with…
2A5S 1.7 Å, Crystal Structure Of The NR2A Ligand Binding Core In Complex With Glutamate
5I57 1.7 Å, Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains
9NYZ 1.71 Å, Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with…
4NF8 1.86 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and…
6UZR 1.87 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…
4NF5 1.9 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and D-AP5
6UZG 1.94 Å, Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with…
5VII 1.95 Å, Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and…

Browse structure collections

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