1KJ2: Allogeneic H-2Kb MHC Class I Molecule

Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex. Determined by X-ray diffraction at 2.71 Å resolution. Released 27 Mar 2002.

Method: X-ray diffraction
Resolution: 2.71 Å
Organism: Mus musculus
Chains: 10
Atoms: 10,144
Mol. weight: 142.98 kDa
Ligands: NAG
Released: 27 Mar 2002

Explore 1KJ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1KJ2 contains 23 α-helices and 105 β-strands across 9 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: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	9-13	5	8
β-strand	18-24	7	7
β-strand	29-37	9	8
β-strand	44-50	7	8
β-strand	55-58	4	7
β-strand	62-67	6	7
β-strand	72-77	6	7
β-strand	86-90	5	8
β-strand	91-92	2	9
β-strand	93-94	2	8
β-strand	105-106	2	9
β-strand	110-115	6	8

Chains B and E: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	31-38	8	11
β-strand	43-49	7	11
β-strand	55-60	6	10
β-strand	63-69	7	10
β-strand	74-80	7	10
β-strand	86-95	8	11
β-strand	112-116	5	11

Chain D: 0 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	18
β-strand	6	1	19
β-strand	9-12	4	20
β-strand	18-23	6	19
β-strand	24	1	18
β-strand	29-37	9	20
β-strand	44-50	7	20
β-strand	55-58	4	19
β-strand	62-67	6	19
β-strand	72-77	6	19
β-strand	87-90	4	20
β-strand	91-92	2	21
β-strand	93-94	2	20
β-strand	105-106	2	21
β-strand	110-114	5	20

Chain H: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	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	139-149	11
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-179	15
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	222-223	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 I: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	12
α-helix	19-20	2
β-strand	21-28	8	12
β-strand	31-37	7	12
β-strand	46-47	2	12
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	12
β-strand	109-118	10	12
β-strand	121-126	6	12
β-strand	133-135	3	12
α-helix	139-149	11
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-179	15
β-strand	183	1	13
β-strand	186-194	9	14
β-strand	198-208	11	14
β-strand	209	1	13
β-strand	214-219	6	15
β-strand	222-223	2	15
β-strand	229-230	2	14
α-helix	231-233	3
β-strand	234-235	2	14
β-strand	241-250	10	14
β-strand	257-262	6	15
β-strand	270-272	3	15

Chain L: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6-11	6	5
β-strand	21-30	10	5
β-strand	36-41	6	6
β-strand	44-45	2	6
α-helix	46	1
β-strand	50-51	2	5
α-helix	52-54	3
β-strand	55-56	2	5
β-strand	62-70	9	5
β-strand	78-83	6	6
β-strand	91-94	4	6

Chain M: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6	1	16
β-strand	9-11	3	16
β-strand	21-30	10	16
β-strand	36-41	6	17
β-strand	44-45	2	17
α-helix	46	1
β-strand	50	1	16
β-strand	55-56	2	16
β-strand	62-70	9	16
β-strand	78-83	6	17
β-strand	91-94	4	17

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Allogeneic H-2Kb MHC Class I Molecule	H, I	protein	277	Mus musculus	P01901 (AlphaFold model)
Naturally processed octapeptide PKB1	P, Q	protein	8		O08582 (AlphaFold model)
Beta-2 microglobulin	L, M	protein	99	Mus musculus	P01887 (AlphaFold model)
KB5-C20 T-Cell receptor alpha-chain	A, D	protein	111	Mus musculus
KB5-C20 T-Cell receptor beta-chain	B, E	protein	117	Mus musculus	P04214 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>1KJ2_1 Allogeneic H-2Kb MHC Class I Molecule (chains H, I)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPP

Sequence of entity 2 (P, Q), FASTA

>1KJ2_2 Naturally processed octapeptide PKB1 (chains P, Q)
KVITFIDL

Sequence of entity 3 (L, M), FASTA

>1KJ2_3 Beta-2 microglobulin (chains L, M)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 4 (A, D), FASTA

>1KJ2_4 KB5-C20 T-Cell receptor alpha-chain (chains A, D)
QQVRQSPQSLTVWEGETAILNCSYEDSTFNYFPWYQQFPGEGPALLISIRSVSDKKEDGR
FTIFFNKREKKLSLHITDSQPGDSATYFCAARYQGGRALIFGTGTTVSVSP

Sequence of entity 5 (B, E), FASTA

>1KJ2_5 KB5-C20 T-Cell receptor beta-chain (chains B, E)
VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKS
LPGADYLATRVTDTELRLQVANMSQGRTLYCTCSAAPDWGASAETLYFGSGTRLTVL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex. Reiser, J.B., Gregoire, C., Darnault, C. et al. Immunity (2002) 16:345-354. DOI 10.1016/S1074-7613(02)00288-1 · PubMed

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

1LK2 1.35 Å, 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
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

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