5XEQ: Human MDGA1 and human neuroligin-2 complex

Crystal Structure of human MDGA1 and human neuroligin-2 complex. Determined by X-ray diffraction at 3.14 Å resolution. Released 12 Jul 2017.

Method: X-ray diffraction
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,450
Mol. weight: 100.23 kDa
Ligands: NAG
Released: 12 Jul 2017

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

Secondary structure: helices and β-sheets

5XEQ contains 34 α-helices and 47 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: 26 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	1
β-strand	50-52	3	1
β-strand	54-57	4	2
β-strand	65-73	9	2
β-strand	96-98	3	1
β-strand	100	1	2
α-helix	102-104	3
β-strand	105	1	3
α-helix	106	1
α-helix	121-125	5
α-helix	127-131	5
α-helix	132-134	3
β-strand	137	1	3
β-strand	143-148	6	2
β-strand	177-183	7	2
α-helix	193-195	3
α-helix	199-205	7
β-strand	208-212	5	2
α-helix	217-221	5
α-helix	233-246	14
α-helix	249-252	4
β-strand	254-264	11	2
α-helix	266-276	11
β-strand	286-290	5	2
β-strand	301	1	4
α-helix	304-314	11
α-helix	322-329	8
α-helix	334-338	5
β-strand	354	1	4
α-helix	364-369	6
β-strand	377-383	7	2
α-helix	388-391	4
α-helix	403-417	15
α-helix	424-434	11
α-helix	444-455	12
α-helix	456-461	6
α-helix	462-473	12
β-strand	478-483	6	2
β-strand	489	1	5
β-strand	492	1	5
α-helix	504-507	4
α-helix	510-512	3
α-helix	525-544	20
β-strand	573	1	2
β-strand	580-583	4	2
β-strand	588-590	3	2
α-helix	595-599	5
α-helix	600-604	5

Chain B: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	6
β-strand	47-51	5	7
α-helix	55	1
β-strand	56-63	8	6
α-helix	68	1
β-strand	69-74	6	7
β-strand	88	1	7
β-strand	92-95	4	6
α-helix	100-102	3
β-strand	105-111	7	7
α-helix	117	1
β-strand	118-127	10	7
β-strand	133-137	5	8
β-strand	153-158	6	8
α-helix	164-165	2
β-strand	166-171	6	9
β-strand	175	1	9
β-strand	184-187	4	8
β-strand	196-201	6	8
β-strand	211-217	7	9
α-helix	224-226	3
β-strand	227-232	6	9
β-strand	241-244	4	10
β-strand	249-252	4	11
β-strand	258-261	4	12
β-strand	262-266	5	10
β-strand	272-274	3	11
β-strand	286	1	12
β-strand	292-295	4	12
α-helix	300-302	3
β-strand	304-311	8	11
α-helix	317	1
β-strand	318-326	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuroligin-2	A	protein	576	Homo sapiens	Q8NFZ4 (AlphaFold model)
MAM domain-containing glycosylphosphatidylinositol anchor protein 1	B	protein	319	Homo sapiens	Q8NFP4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5XEQ_1 Neuroligin-2 (chains A)
ADPPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRQ
ATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKK
RDEATLNPPDTDIRDPGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVATLNYRLGV
LGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSH
HSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSAEAVECLRRKPSRELV
DQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESE
DGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDH
QWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDL
FPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEK
QYLHIGLKPRVRDNYRANKVAFWLELVPHLHNLVPR

Sequence of entity 2 (B), FASTA

>5XEQ_2 MAM domain-containing glycosylphosphatidylinositol anchor protein 1 (chains B)
ADPQGVYAPAQAQIVHAGQACVVKEDNISERVYTIREGDTLMLQCLVTGHPRPQVRWTKT
AGSASDKFQETSVFNETLRIERIARTQGGRYYCKAENGVGVPAIKSIRVDVQYLDEPMLT
VHQTVSDVRGNFYQEKTVFLRCTVNSNPPARFIWKRGSDTLSHSQDNGVDIYEPLYTQGE
TKVLKLKNLRPQDYASYTCQVSVRNVCGIPDKAITFRLTNTTAPPALKLSVNETLVVNPG
ENVTVQCLLTGGDPLPQLQWSHGPGPLPLGALAQGGTLSIPSVQARDSGYYNCTATNNVG
NPAKKTVNLLVRSMKLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Structural Insights into Modulation of Neurexin-Neuroligin Trans-synaptic Adhesion by MDGA1/Neuroligin-2 Complex. Kim, J.A., Kim, D., Won, S.Y. et al. Neuron (2017) 94:1121-1131.e6. DOI 10.1016/j.neuron.2017.05.034 · PubMed

Other PDB entries of the same protein (UniProt Q8NFZ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FAJ 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…
9FAK 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…
9FAP 2.8 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4,…
9FAN 2.9 Å, CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of…
9FAQ 2.9 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4,…
9FAR 2.9 Å, CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of…
9FAW 2.9 Å, CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with…
9FAX 2.9 Å, CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with…
9FAU 3.1 Å, CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with…
9RGE 3.1 Å, CryoEM structure of human alpha1beta3gamma2 GABA(A)R in complex with GARLH4 and the…
9FAV 3.2 Å, CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with…
8GS4 3.5 Å, Cryo-EM structure of human Neuroligin 2

Browse structure collections

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