1NAN: Mch class I H-2KB molecule

Mch class I H-2KB molecule complexed with PBM1 peptide. Determined by X-ray diffraction at 2.3 Å resolution. Released 11 Mar 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,462
Mol. weight: 89.51 kDa
Released: 11 Mar 2003

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

Secondary structure: helices and β-sheets

1NAN contains 24 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 H: 10 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	159-164	6
α-helix	165-174	10
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	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 I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain L: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	5
α-helix	20	1
β-strand	21-28	8	5
β-strand	31-37	7	5
β-strand	46-47	2	5
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	5
β-strand	109-118	10	5
β-strand	121-126	6	5
β-strand	133-135	3	5
α-helix	140-149	10
α-helix	153-158	6
α-helix	159-163	5
α-helix	164-175	12
β-strand	183	1	6
α-helix	184-185	2
β-strand	186-193	8	7
β-strand	198-208	11	7
β-strand	209	1	6
β-strand	214-219	6	8
β-strand	222-223	2	8
α-helix	225-227	3
β-strand	229-230	2	7
α-helix	231-233	3
β-strand	234-235	2	7
β-strand	241-250	10	7
α-helix	254-256	3
β-strand	257-262	6	8
β-strand	270-272	3	8

Chain P: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
β-strand	6-11	6	10
β-strand	21-30	10	10
β-strand	31	1	9
β-strand	36-41	6	11
β-strand	44-45	2	11
α-helix	46	1
β-strand	50-51	2	10
β-strand	55-56	2	10
β-strand	62-70	9	10
β-strand	78-83	6	11
β-strand	91-94	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, K-B alpha chain	H, L	protein	278	Mus musculus	P01901 (AlphaFold model)
Beta-2-microglobulin	I, P	protein	99	Mus musculus	P01887 (AlphaFold model)
pBM1 peptide	M, Q	protein	8		Q8CDD8 (AlphaFold model)

Sequence of entity 1 (H, L), FASTA

>1NAN_1 H-2 class I histocompatibility antigen, K-B alpha chain (chains H, L)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPP

Sequence of entity 2 (I, P), FASTA

>1NAN_2 Beta-2-microglobulin (chains I, P)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (M, Q), FASTA

>1NAN_3 pBM1 peptide (chains M, Q)
INFDFNTI

Primary citation

CDR3 loop flexibility contributes to the degeneracy of TCR recognition. Reiser, J.-B., Darnault, C., Gregoire, C. et al. Nat Immunol (2003) 4:241-247. DOI 10.1038/ni891 · 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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