5KDT: Human GluN1/GluN2A LBD

Structure of the human GluN1/GluN2A LBD in complex with GNE0723. Determined by X-ray diffraction at 2.44 Å resolution. Released 13 Jul 2016.

Method: X-ray diffraction
Resolution: 2.44 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,607
Mol. weight: 66.04 kDa
Ligands: GLU, 6RV, GLY
Released: 13 Jul 2016

Explore 5KDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KDT contains 31 α-helices and 39 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	7-12	6	1
β-strand	15	1	2
β-strand	19	1	2
β-strand	20-23	4	1
α-helix	24-25	2
β-strand	36-43	8	1
β-strand	51-59	9	1
α-helix	61-72	12
β-strand	76-81	6	1
β-strand	90-91	2	3
β-strand	94-95	2	3
α-helix	97-103	7
β-strand	109-110	2	1
β-strand	115	1	4
α-helix	118-121	4
β-strand	125-126	2	1
β-strand	131-140	10	4
α-helix	151-154	4
α-helix	156-158	3
α-helix	162-163	2
β-strand	165-166	2	4
α-helix	172-180	9
α-helix	182-188	7
α-helix	189-191	3
α-helix	196-204	9
β-strand	210-214	5	4
α-helix	215-223	9
β-strand	230-232	3	4
α-helix	233-236	4
β-strand	239-244	6	4
β-strand	247-248	2	1
α-helix	255-268	14
α-helix	270-278	9

Chain B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7-11	5	5
β-strand	14	1	6
β-strand	18	1	6
β-strand	19-22	4	5
α-helix	23-24	2
α-helix	29-31	3
β-strand	33	1	7
α-helix	38	1
β-strand	39	1	7
α-helix	40-41	2
β-strand	43-48	6	5
β-strand	59-65	7	5
α-helix	67-79	13
β-strand	83-87	5	5
β-strand	96-98	3	8
β-strand	105-107	3	8
α-helix	109-115	7
β-strand	121-122	2	5
β-strand	127	1	9
α-helix	130-133	4
β-strand	136-138	3	5
β-strand	143-152	10	9
α-helix	163-166	4
β-strand	174-175	2	9
β-strand	177	1	10
α-helix	181-188	8
α-helix	190-192	3
α-helix	193-200	8
β-strand	204	1	10
α-helix	207-215	9
β-strand	221-225	5	9
α-helix	226-233	8
β-strand	239-251	13	9
β-strand	254-256	3	5
α-helix	262-274	13
α-helix	277-285	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 2A	A	protein	285	Homo sapiens	Q12879 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 1	B	protein	293	Homo sapiens	Q05586 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5KDT_1 Glutamate receptor ionotropic, NMDA 2A (chains A)
GSPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKG
FCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEER
SEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNN
YPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFA
TTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHN

Sequence of entity 2 (B), FASTA

>5KDT_2 Glutamate receptor ionotropic, NMDA 1 (chains B)
GSMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTV
PQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQAD
MIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQS
SVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLV
TTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	1
6RV	(1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxid…	C16 H8 Cl F6 N5 O S	1
GLY	Glycine	C2 H5 N O2	1

Water and common crystallization additives (ACT) are not listed.

Primary citation

Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design. Volgraf, M., Sellers, B.D., Jiang, Y. et al. J Med Chem (2016) 59:2760-2779. DOI 10.1021/acs.jmedchem.5b02010 · PubMed

Other PDB entries of the same protein (UniProt Q12879 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5H8F 1.81 Å, Structure of the apo human GluN1/GluN2A LBD
5H8Q 1.9 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE8324
3NFL 1.91 Å, Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A…
9MUM 1.97 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11,…
5KCJ 2.09 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE6901
5I2N 2.12 Å, Structure of the human GluN1/GluN2A LBD in complex with…
5H8H 2.23 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE3419
5TP9 2.4 Å, Structure of the human GluN1/GluN2A LBD in complex with compound 2 (GNE9178)
9MUL 2.4 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1,…
5TPA 2.48 Å, Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)
5H8N 2.5 Å, Structure of the human GluN1/GluN2A LBD in complex with NAM
5I2K 2.86 Å, Structure of the human GluN1/GluN2A LBD in complex with…

Browse structure collections

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