2X6M: Single domain camelid antibody fragment

Structure of a single domain camelid antibody fragment in complex with a C-terminal peptide of alpha-synuclein. Determined by X-ray diffraction at 1.62 Å resolution. Released 23 Jun 2010.

Method: X-ray diffraction
Resolution: 1.62 Å
Organisms: CAMELUS DROMEDARIUS, HOMO SAPIENS
Chains: 2
Atoms: 1,235
Mol. weight: 14.51 kDa
Released: 23 Jun 2010

Explore 2X6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2X6M contains 5 α-helices and 11 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-13	4	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	59-61	3	2
α-helix	63-65	3
β-strand	69-74	6	1
α-helix	75-77	3
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-100	8	2
β-strand	113-116	4	2
β-strand	120-125	6	2

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	137-139	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain variable domain from dromedary	A	protein	126	CAMELUS DROMEDARIUS
Alpha-synuclein peptide	B	protein	9	HOMO SAPIENS	P37840 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2X6M_1 HEAVY CHAIN VARIABLE DOMAIN FROM DROMEDARY (chains A)
GQLVESGGGSVQAGGSLRLSCAASGIDSSSYCMGWFRQRPGKEREGVARINGLGGVKTAY
ADSVKDRFTISRDNAENTVYLQMNSLKPEDTAIYYCAAKFSPGYCGGSWSNFGYWGQGTQ
VTVSSH

Sequence of entity 2 (B), FASTA

>2X6M_2 ALPHA-SYNUCLEIN PEPTIDE (chains B)
GYQDYEPEA

Primary citation

Structure and Properties of a Complex of Alpha-Synuclein and a Single-Domain Camelid Antibody. De Genst, E.J., Guilliams, T., Wellens, J. et al. J Mol Biol (2010) 402:326. DOI 10.1016/J.JMB.2010.07.001 · PubMed

Other PDB entries of the same protein (UniProt P37840 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JJV 1.23 Å, Structure of truncated form of nanobody in complex with alpha-synuclein peptide
8JLY 1.29 Å, Structure of nanobody in complex with alpha-synuclein peptide
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
4R0U 1.38 Å, Tgvtava, an amyloid forming segment from alpha synuclein, residues 72-78
6I42 1.38 Å, Structure of the alpha-Synuclein PreNAC/Cyclophilin A-complex
4ZNN 1.41 Å, MicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of…
4RIL 1.43 Å, Structure of the amyloid forming segment, GAVVTGVTAVA, from the NAC domain of…
4R0W 1.5 Å, Vvtgvta, an amyloid forming segment from alpha synuclein, residues 70-76
3Q26 1.54 Å, Cyrstal structure of human alpha-synuclein (10-42) fused to maltose binding protein (MBP)
3Q28 1.6 Å, Cyrstal structure of human alpha-synuclein (58-79) fused to maltose binding protein (MBP)
5CRW 1.6 Å, Crystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed…
8OG0 1.71 Å, Crystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide

Browse structure collections

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