6V2Q: HLA-B*57:03 presenting the peptide LSSPVTKSF

HLA-B*57:03 presenting the peptide LSSPVTKSF. Determined by X-ray diffraction at 1.6 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,928
Mol. weight: 44.72 kDa
Released: 20 May 2020

Explore 6V2Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V2Q 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	152-161	10
α-helix	163-174	12
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
α-helix	225-227	3
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: 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
HLA-B alpha chain (B*5703GB)	A	protein	276	Homo sapiens	I3ZN84 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Peptide LEU-SER-SER-PRO-VAL-THR-LYS-SER-PHE	C	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>6V2Q_1 HLA-B alpha chain (B*5703GB) (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYW
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHNQYAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6V2Q_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6V2Q_3 Peptide LEU-SER-SER-PRO-VAL-THR-LYS-SER-PHE (chains C)
LSSPVTKSF

Primary citation

The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function. Saunders, P.M., MacLachlan, B.J., Pymm, P. et al. Proc Natl Acad Sci U S A (2020) 117:11636-11647. DOI 10.1073/pnas.1920570117 · 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
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
5VVP 2.0 Å, HLA-B*57:03 presenting LSSPVTKSW
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

Browse structure collections

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