3KYO: HLA-G presenting KLPAQFYIL peptide

Crystal structure of HLA-G presenting KLPAQFYIL peptide. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Feb 2010.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,283
Mol. weight: 89.27 kDa
Ligands: CO
Released: 23 Feb 2010

Explore 3KYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KYO contains 29 α-helices and 60 β-strands across 4 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: 11 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	111-118	8	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	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-224	3	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

Chains B and D: 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

Chain C: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-194	9	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
α-helix	224	1
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, C	protein	273	Homo sapiens	P17693 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
KLPAQFYIL peptide	P, Q	protein	9

Sequence of entity 1 (A, C), FASTA

>3KYO_1 MHC class I antigen (chains A, C)
SHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQFVRFDSDSASPRMEPRAPWVEQEGPEYWE
EETRNTKAHAQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLIRGYERYAYDGK
DYLALNEDLRSWTAADTAAQISKRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEMLQR
ADPPKTHVTHHPVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDGTF
QKWAAVVVPSGEEQRYTCHVQHEGLPEPLMLRW

Sequence of entity 2 (B, D), FASTA

>3KYO_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P, Q), FASTA

>3KYO_3 KLPAQFYIL peptide (chains P, Q)
KLPAQFYIL

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	2

Primary citation

The structure and stability of the monomorphic HLA-G are influenced by the nature of the bound peptide. Walpole, N.G., Kjer-Nielsen, L., Kostenko, L. et al. J Mol Biol (2010) 397:467-480. DOI 10.1016/j.jmb.2010.01.052 · PubMed

Other PDB entries of the same protein (UniProt P17693 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1YDP 1.9 Å, 1.9A crystal structure of HLA-G
3KYN 2.4 Å, Crystal structure of HLA-G presenting KGPPAALTL peptide
2DYP 2.5 Å, Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G
3BZE 2.5 Å, The human non-classical major histocompatibility complex molecule HLA-E
6K60 3.15 Å, Structural and functional basis for HLA-G isoform recognition of immune checkpoint…
2D31 3.2 Å, Crystal structure of disulfide-linked HLA-G dimer
6AEE 3.3 Å, Crystal structure of the four Ig-like domains of LILRB1 complexed with HLA-G
3CDG 3.4 Å, Human CD94/NKG2A in complex with HLA-E
9RWI 3.45 Å, crystal structure of a human leukocyte antigen-A (HLA-G) blocking antibody
3CII 4.41 Å, Structure of NKG2A/CD94 bound to HLA-E

Browse structure collections

About this viewer

MolViewer shows 3KYO 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.