1LK2: 1.35A crystal structure of H-2Kb

1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide. Determined by X-ray diffraction at 1.35 Å resolution. Released 11 Nov 2003.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,636
Mol. weight: 45.32 kDa
Ligands: MRD, PO4, NAG
Released: 11 Nov 2003

Explore 1LK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LK2 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: 9 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	57-84	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	138-150	13
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
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
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, 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
α-helix	49	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
H-2 class I histocompatibility antigen, K-B alpha chain	A	protein	274	Mus musculus	P01901 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
Insulin receptor, beta-subunit	P	protein	8		P15208 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1LK2_1 H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN (chains A)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>1LK2_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>1LK2_3 INSULIN RECEPTOR, BETA-SUBUNIT (chains P)
GNYSFYAL

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	1
PO4	Phosphate ion	O4 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (MPD) are not listed.

Primary citation

A peptide that antagonizes TCR-mediated reactions with both syngeneic and allogeneic agonists: functional and structural aspects. Rudolph, M.G., Shen, L.Q., Lamontagne, S.A. et al. J Immunol (2004) 172:2994-3002. PubMed

Other PDB entries of the same protein (UniProt P01901 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1G7P 1.5 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
1KPU 1.5 Å, High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3TID 1.65 Å, Crystal structure of the LCMV derived peptide GP34 in complex with the murine mhc class…
1FZK 1.7 Å, MHC class I natural mutant H-2KBM1 heavy chain complexed with beta-2 microglobulin and…
1KPV 1.71 Å, High resolution crystal structure of the MHC class I complex H-2Kb/SEV9
1LEG 1.75 Å, Crystal Structure of H-2Kb bound to the dEV8 peptide
6GB6 1.78 Å, Structure of H-2Kb with dipeptide GL
1FZM 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1FZO 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1T0N 1.8 Å, Conformational switch in polymorphic H-2K molecules containing an HSV peptide
2QRT 1.8 Å, Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy…

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