3BL8: Extracellular domain of neuroligin 2A from mouse

Crystal structure of the extracellular domain of neuroligin 2A from mouse. Determined by X-ray diffraction at 3.3 Å resolution. Released 19 Feb 2008.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Mus musculus
Chains: 4
Atoms: 17,374
Mol. weight: 261.67 kDa
Ligands: NAG
Released: 19 Feb 2008

Explore 3BL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BL8 contains 110 α-helices and 77 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: 31 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	1
β-strand	50-51	2	1
β-strand	55-56	2	2
α-helix	64-65	2
β-strand	66-73	8	2
α-helix	89-91	3
β-strand	96-97	2	1
α-helix	102-104	3
β-strand	105	1	3
α-helix	121-125	5
α-helix	127-131	5
α-helix	132-134	3
β-strand	137	1	3
β-strand	143-149	7	2
α-helix	175-176	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	233-248	16
α-helix	249-252	4
β-strand	254-264	11	2
α-helix	266-276	11
β-strand	286-290	5	2
α-helix	304-315	12
α-helix	322-329	8
α-helix	334-338	5
α-helix	364-370	7
β-strand	377-383	7	2
α-helix	390-394	5
β-strand	400	1	4
α-helix	403-416	14
α-helix	424-435	12
α-helix	444-455	12
α-helix	456-461	6
α-helix	462-473	12
β-strand	478-484	7	2
α-helix	504-508	5
α-helix	510-513	4
α-helix	525-544	20
α-helix	552-553	2
α-helix	564-566	3
β-strand	579-584	6	2
β-strand	589-591	3	2
α-helix	595-599	5
α-helix	600-604	5
α-helix	606-608	3

Chain B: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	43-46	4	5
β-strand	49-52	4	5
β-strand	54-56	3	6
β-strand	66-69	4	6
β-strand	70	1	7
β-strand	71-73	3	6
α-helix	86-92	7
β-strand	96-98	3	5
β-strand	100	1	7
α-helix	102-104	3
β-strand	105	1	8
α-helix	106-107	2
α-helix	121-125	5
α-helix	127-131	5
β-strand	137	1	8
β-strand	143-149	7	6
β-strand	177-183	7	6
α-helix	199-203	5
β-strand	208-212	5	6
α-helix	217-220	4
α-helix	233-248	16
α-helix	249-252	4
β-strand	254-264	11	6
α-helix	266-276	11
β-strand	286-290	5	6
α-helix	304-315	12
α-helix	322-329	8
α-helix	334-338	5
α-helix	343-344	2
α-helix	364-369	6
β-strand	377-383	7	6
α-helix	386-394	9
α-helix	407-415	9
α-helix	421-423	3
α-helix	426-434	9
α-helix	446-456	11
α-helix	457-461	5
α-helix	462-473	12
β-strand	478-484	7	6
β-strand	489	1	9
α-helix	504-507	4
β-strand	521	1	9
α-helix	525-544	20
β-strand	580-584	5	6
β-strand	588-590	3	6
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-607	3

Chain C: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	43-46	4	10
β-strand	49-52	4	10
β-strand	54-57	4	11
β-strand	65-73	9	11
α-helix	80-82	3
α-helix	102-104	3
β-strand	105	1	12
α-helix	106	1
α-helix	121-125	5
α-helix	127-130	4
α-helix	131-134	4
β-strand	137	1	12
β-strand	143-149	7	11
β-strand	177-183	7	11
α-helix	193-195	3
α-helix	199-205	7
β-strand	208-210	3	11
β-strand	212	1	11
α-helix	233-248	16
α-helix	249-252	4
β-strand	254-264	11	11
α-helix	266-276	11
β-strand	286-290	5	11
α-helix	304-315	12
α-helix	322-329	8
α-helix	334-338	5
α-helix	364-370	7
β-strand	377-383	7	11
α-helix	388-391	4
α-helix	403-417	15
α-helix	423-434	12
α-helix	445-456	12
α-helix	457-461	5
α-helix	462-473	12
β-strand	478-483	6	11
α-helix	504-507	4
α-helix	525-544	20
β-strand	580-583	4	11
β-strand	588-590	3	11
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-607	3

Chain D: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	13
β-strand	50-52	3	13
β-strand	54-56	3	14
β-strand	66-69	4	14
β-strand	70	1	15
β-strand	71-73	3	14
α-helix	90-92	3
β-strand	96-98	3	13
β-strand	100	1	15
α-helix	102-104	3
β-strand	105	1	16
α-helix	106	1
α-helix	121-125	5
α-helix	127-133	7
β-strand	137	1	16
β-strand	143-149	7	14
β-strand	177-183	7	14
α-helix	193-195	3
α-helix	198-205	8
β-strand	208-211	4	14
α-helix	217-219	3
α-helix	233-248	16
β-strand	254-263	10	14
α-helix	266-275	10
β-strand	286-290	5	14
α-helix	297-299	3
β-strand	301	1	17
α-helix	304-315	12
α-helix	322-329	8
α-helix	334-338	5
β-strand	354	1	17
α-helix	364-369	6
β-strand	377-383	7	14
α-helix	388-390	3
β-strand	401	1	18
α-helix	403-417	15
α-helix	424-434	11
β-strand	444	1	18
α-helix	445-456	12
α-helix	457-461	5
α-helix	462-472	11
β-strand	478-484	7	14
α-helix	504-508	5
α-helix	525-544	20
α-helix	571-573	3
β-strand	580-584	5	14
β-strand	589-590	2	14
α-helix	595-602	8
α-helix	606-608	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuroligin-2	A, B, C, D	protein	580	Mus musculus	Q69ZK9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3BL8_1 Neuroligin-2 (chains A, B, C, D)
QKPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNA
TTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKR
DEATLNPPDTDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVVTLNYRLGVL
GFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHH
SEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVD
QDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESED
GVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQ
WVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLF
PCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQ
YLHIGLKPRVRDNYRANKVAFWLELVPHLHNLHHHHHHHH

Ligands and cofactors

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

Primary citation

Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Koehnke, J., Jin, X., Budreck, E.C. et al. Proc Natl Acad Sci U S A (2008) 105:1873-1878. DOI 10.1073/pnas.0711701105 · PubMed

Other PDB entries of the same protein (UniProt Q69ZK9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G7Z 3.22 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta…
8G81 3.22 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta…
8G80 3.25 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta…
8G7D 3.28 Å, Cryo-EM structure of full length Neuroligin-2 from Mouse
8G7Y 3.92 Å, Cryo-EM Structure of full length Neuroligin-2 from mouse with Neurexin-1 beta

Browse structure collections

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