1LD9: MHC class I H-2LD heavy chain

The three-dimensional structure of an H-2LD peptide complex explains the unique interaction of ld with BETA2M and peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 6 May 1998.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,168
Mol. weight: 87.57 kDa
Released: 6 May 1998

Explore 1LD9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LD9 contains 14 α-helices and 58 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.

Chains A and D: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	1
α-helix	50-53	4
α-helix	58-84	27
β-strand	94-102	9	1
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	132-135	4	1
α-helix	140-149	10
α-helix	153-160	8
α-helix	163-173	11
α-helix	177-180	4
β-strand	191-192	2	2
β-strand	199-204	6	2
β-strand	208	1	3
β-strand	214-218	5	4
β-strand	223	1	4
β-strand	230	1	2
β-strand	234-236	3	5
β-strand	238-242	5	5
β-strand	244-249	6	2
β-strand	258-262	5	4

Chains B and E: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
β-strand	6	1	7
β-strand	9-11	3	7
β-strand	22-28	7	7
β-strand	31	1	6
β-strand	36-40	5	8
β-strand	45	1	8
β-strand	50-56	7	7
β-strand	62-69	8	7
β-strand	79-83	5	8
β-strand	91-94	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I H-2LD heavy chain	A, D	protein	268	Mus musculus	P01897 (AlphaFold model)
Beta-2 microglobulin	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)
Nano-peptide	C, F	protein	9

Sequence of entity 1 (A, D), FASTA

>1LD9_1 MHC CLASS I H-2LD HEAVY CHAIN (chains A, D)
GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYW
ERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDG
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPE

Sequence of entity 2 (B, E), FASTA

>1LD9_2 BETA-2 MICROGLOBULIN (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F), FASTA

>1LD9_3 NANO-PEPTIDE (chains C, F)
YPNVNIHNF

Primary citation

The three-dimensional structure of an H-2Ld-peptide complex explains the unique interaction of Ld with beta-2 microglobulin and peptide. Balendiran, G.K., Solheim, J.C., Young, A.C. et al. Proc Natl Acad Sci U S A (1997) 94:6880-6885. DOI 10.1073/pnas.94.13.6880 · PubMed

Other PDB entries of the same protein (UniProt P01897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
6L9K 1.8 Å, H2-Ld a1a2 complexed with A5 peptide
8D5N 1.8 Å, Crystal structure of Ld-HF10
3VJ6 1.9 Å, Structure of the MHC class Ib molecule Qa-1b
4MS8 1.92 Å, 42F3 TCR pCPB9/H-2Ld Complex
3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
5VCL 2.05 Å, Structure of the Qdm peptide bound to Qa-1a
3TJH 2.12 Å, 42F3-p3A1/H2-Ld complex
2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex

Browse structure collections

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