5TPW: NMDA glutamate receptor subunit

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A. Determined by X-ray diffraction at 2.91 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Xenopus laevis, Rattus norvegicus, Mus musculus
Chains: 4
Atoms: 8,358
Mol. weight: 132.95 kDa
Ligands: ZN, NAG
Released: 14 Dec 2016

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

Secondary structure: helices and β-sheets

5TPW contains 44 α-helices and 75 β-strands across 4 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: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	1
α-helix	36-51	16
β-strand	58-66	9	1
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	94-96	3
α-helix	105-113	9
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-147	4
α-helix	148-157	10
β-strand	163-168	6	2
α-helix	171-185	15
β-strand	213-218	6	2
α-helix	226-233	8
β-strand	239-243	5	2
α-helix	246-256	11
β-strand	267-269	3	2
α-helix	273-275	3
α-helix	278-281	4
α-helix	283-284	2
β-strand	288-292	5	2
α-helix	300-316	17
α-helix	323-326	4
α-helix	335-336	2
α-helix	339-347	9
β-strand	350-351	2	3
β-strand	359-361	3	3
β-strand	367-368	2	3
β-strand	372-378	7	2
β-strand	381-388	8	2
β-strand	393-395	3	2
α-helix	396	1
β-strand	400-401	2	4
β-strand	407-408	2	4

Chain B: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	5
β-strand	68-73	6	5
α-helix	79-90	12
β-strand	97-101	5	5
α-helix	108-120	13
β-strand	124-128	5	5
α-helix	129-132	4
α-helix	137-139	3
β-strand	144-146	3	5
α-helix	151-164	14
β-strand	169-174	6	6
α-helix	180-192	13
β-strand	199-200	2	6
α-helix	201-203	3
β-strand	204-205	2	6
α-helix	212-219	8
β-strand	226-230	5	6
α-helix	233-245	13
β-strand	254-257	4	6
α-helix	259-262	4
α-helix	273	1
β-strand	277-280	4	6
α-helix	288-305	18
α-helix	314-317	4
β-strand	342-343	2	7
β-strand	346-347	2	7
β-strand	350	1	8
β-strand	356	1	8
β-strand	362-367	6	6
β-strand	371-377	7	6

Chain H: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-52	8	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	106-109	4	10
β-strand	113-117	5	10
β-strand	127-130	4	11
β-strand	141-151	11	11
β-strand	157-160	4	12
α-helix	161-163	3
β-strand	165	1	12
β-strand	169-171	3	11
α-helix	172-174	3
β-strand	175-176	2	11
β-strand	181-190	10	11
α-helix	191-193	3
β-strand	200-205	6	12
β-strand	210-215	6	12

Chain L: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-46	2	14
β-strand	62-66	5	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-155	3	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-181	9	16
α-helix	183-188	6
β-strand	191-197	7	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NMDA glutamate receptor subunit	A	protein	389	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B	protein	360	Rattus norvegicus	Q00959 (AlphaFold model)
FAB, heavy chain	H	protein	221	Mus musculus
FAB, light chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>5TPW_1 NMDA glutamate receptor subunit (chains A)
PKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLI
SSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPP
YSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLS
YDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTG
AGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENIT
DPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLV
QVGIFNGSYIIQNDRKIIWPGGETEGTLV

Sequence of entity 2 (B), FASTA

>5TPW_2 Glutamate receptor ionotropic, NMDA 2A (chains B)
LNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGA
RIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQ
QATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDA
KTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFP
SGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQAEKPETPLHT
LHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRY

Sequence of entity 3 (H), FASTA

>5TPW_3 FAB, HEAVY CHAIN (chains H)
EVKLVESGPELKKPGETVKISCKASGFTFTNYGMNWVKQAPGKGLKWMGWINIYTGEPTY
ADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCARGYDYEGYFDYWGQGTTLTVSSA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 4 (L), FASTA

>5TPW_4 FAB, LIGHT CHAIN (chains L)
DIVMTQAPATLSVTPGDRVSLSCRASQSIADYLYWYQQKSHESPRLLLKYASQSISGIPS
RFSGSGSGSDFTLTINSVEPEDVGMYYCQNGHSFPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLAAGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

Primary citation

Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Romero-Hernandez, A., Simorowski, N., Karakas, E. et al. Neuron (2016) 92:1324-1336. DOI 10.1016/j.neuron.2016.11.006 · PubMed

Other PDB entries of the same protein (UniProt A0A1L8F5J9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QEK 2.0 Å, Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1
6E7R 2.1 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7U 2.27 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7T 2.31 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7X 2.58 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
3QEL 2.6 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7V 2.6 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7W 2.67 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
5TQ0 2.7 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7S 2.72 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
9Q3Y 2.74 Å, GluN1b-GluN2B ATD in complex with radiprodil
5EWM 2.76 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…

Browse structure collections

About this viewer

MolViewer shows 5TPW directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.