5VCL: Qdm peptide

Structure of the Qdm peptide bound to Qa-1a. Determined by X-ray diffraction at 2.05 Å resolution. Released 25 Oct 2017.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,309
Mol. weight: 45.67 kDa
Released: 25 Oct 2017

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

Secondary structure: helices and β-sheets

5VCL contains 12 α-helices and 29 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-85	29
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-56	7	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H2-T23 protein	A	protein	278	Mus musculus	Q31153 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
Qdm peptide	P	protein	9	Mus musculus	P01897 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VCL_1 H2-T23 protein (chains A)
MSSHSLRYFHTAMSRPGLGEPRFIVVGYVDDTQFVSFDSDSENPKMEPRARWMEQEGPEY
WERETWKARDMGRNFRVNLRTLLGYYNQSKDESHTLQWMYGCDVGPDGRLLRGYCQEAYD
GQDYISLNEDLRSWTATDFASQISKHKSEMVDEAHQQRAYLQGPCVEWLHTYLRLGNKTL
KRSDPPKAHVTHHPRSEDYVTLRCWALGFYPADITLTWQLNGEELTQDMEFVETRPAGDG
NFQKWASVVVPLGKEQNYTCHVEHEGLPEPLTLRWEPP

Sequence of entity 2 (B), FASTA

>5VCL_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>5VCL_3 Qdm peptide (chains P)
AMAPRTLLL

Primary citation

Crystal structure of Qa-1a with bound Qa-1 determinant modifier peptide. Ying, G., Wang, J., Kumar, V. et al. PLoS One (2017) 12:e0182296-e0182296. DOI 10.1371/journal.pone.0182296 · PubMed

Browse structure collections

About this viewer

MolViewer shows 5VCL 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.