5VVP: HLA-B*57:03 presenting LSSPVTKSW

HLA-B*57:03 presenting LSSPVTKSW. Determined by X-ray diffraction at 2.0 Å resolution. Released 3 Oct 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,662
Mol. weight: 44.56 kDa
Released: 3 Oct 2018

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

Secondary structure: helices and β-sheets

5VVP contains 15 α-helices and 30 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: 12 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	50-52	3
α-helix	57-84	28
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
α-helix	182	1
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	228-230	3	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: 3 helices, 11 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	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	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
MHC class I antigen	A	protein	276	Homo sapiens	I3ZN84 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Leu-ser-ser-pro-val-thr-lys-ser-trp	C	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>5VVP_1 MHC class I antigen (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYW
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHNQYAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>5VVP_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>5VVP_3 LEU-SER-SER-PRO-VAL-THR-LYS-SER-TRP (chains C)
LSSPVTKSW

Primary citation

HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Illing, P.T., Pymm, P., Croft, N.P. et al. Nat Commun (2018) 9:4693-4693. DOI 10.1038/s41467-018-07109-w · PubMed

Other PDB entries of the same protein (UniProt I3ZN84 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V2P 1.3 Å, HLA-B*57:03 presenting the peptide ASLNLPAVSW
6V2Q 1.6 Å, HLA-B*57:03 presenting the peptide LSSPVTKSF
9BL4 1.75 Å, KIR3DL1*086 in complex with HLA-B*57:03 presenting the AW10 peptide
6V3J 1.98 Å, KIR3DL1 in complex with HLA-B*57:03 presenting the peptide LSSPVTKSF
9BL3 2.0 Å, KIR3DL1*114 in complex with HLA-B*57:03 presenting the AW10 peptide
9BL2 2.1 Å, KIR3DL1*001 in complex with HLA-B*57:03 presenting the AW10 peptide

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