7MKB: Human leukocyte antigen A*0201

Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 May 2021.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 3,562
Mol. weight: 45.12 kDa
Released: 26 May 2021

Explore 7MKB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MKB contains 14 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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
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
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: 2 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
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	274	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Spike protein S1	C	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7MKB_1 MHC class I antigen (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 2 (B), FASTA

>7MKB_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7MKB_3 Spike protein S1 (chains C)
YLQPRTFLL

Primary citation

Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL. Nyovanie, S.T., Patskovsky, Y., Krogsgaard, M. To be published.

Other PDB entries of the same protein (UniProt A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
7QPJ 1.54 Å, Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10…
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
7U21 1.9 Å, Human Class I MHC HLA-A2 in complex with AVGSYVYSV peptide

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