1D5M: HLA-DR4

X-ray crystal structure of HLA-DR4 complexed with peptide and seb. Determined by X-ray diffraction at 2.0 Å resolution. Released 28 Jun 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Staphylococcus aureus, synthetic construct
Chains: 4
Atoms: 5,076
Mol. weight: 73.15 kDa
Ligands: NAG
Released: 28 Jun 2000

Explore 1D5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D5M contains 23 α-helices and 47 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: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
α-helix	56-58	3
α-helix	59-76	18
α-helix	80-84	5
β-strand	85	1	2
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	113	1	2
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	133-134	2	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	5
α-helix	96-97	2
β-strand	98-103	6	6
β-strand	114-122	9	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-137	2	7
β-strand	142-144	3	6
β-strand	148-149	2	6
β-strand	155-162	8	6
β-strand	170-176	7	7
β-strand	184-189	6	7

Chain C: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	12-13	2
α-helix	14-16	3
β-strand	17	1	8
α-helix	22-28	7
β-strand	33-38	6	9
β-strand	42	1	10
β-strand	48-52	5	10
β-strand	61-67	7	10
α-helix	71-78	8
β-strand	82-86	5	9
β-strand	89	1	10
β-strand	110-115	6	10
β-strand	118-120	3	9
β-strand	125-138	14	11
β-strand	141-152	12	11
β-strand	154-156	3	12
α-helix	157-172	16
β-strand	182-191	10	11
β-strand	194-199	6	11
α-helix	202-203	2
β-strand	205	1	8
α-helix	210-214	5
α-helix	215-217	3
β-strand	222-224	3	12
β-strand	228-236	9	11

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	806-809	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen	A	protein	181	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen	B	protein	192	Homo sapiens	P01911 (AlphaFold model)
Enterotoxin type B	C	protein	239	Staphylococcus aureus	P01552 (AlphaFold model)
Inhibitor	D	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>1D5M_1 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B), FASTA

>1D5M_2 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN (chains B)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN
GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRARS

Sequence of entity 3 (C), FASTA

>1D5M_3 ENTEROTOXIN TYPE B (chains C)
ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGN
YDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTE
HNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNS
PYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

Sequence of entity 4 (D), FASTA

>1D5M_4 INHIBITOR (chains D)
XARAMCSLX

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures. Bolin, D.R., Swain, A.L., Sarabu, R. et al. J Med Chem (2000) 43:2135-2148. DOI 10.1021/jm000034h · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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