1D5X: HLA-DR4

X-ray crystal structure of HLA-DR4 complexed with dipeptide mimetic and seb. Determined by X-ray diffraction at 2.45 Å resolution. Released 28 Jun 2000.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 4
Atoms: 4,910
Mol. weight: 72.76 kDa
Released: 28 Jun 2000

Explore 1D5X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D5X contains 19 α-helices and 49 β-strands across 3 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: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	48-51	4
α-helix	58-76	19
α-helix	82-84	3
β-strand	85	1	2
β-strand	88-93	6	3
β-strand	98	1	4
β-strand	101	1	4
β-strand	103-112	10	3
β-strand	113	1	2
β-strand	118-123	6	5
β-strand	126-127	2	5
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	5
β-strand	174-178	5	5

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	25-32	8	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	55-61	7
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	6
β-strand	98-102	5	7
β-strand	114-122	9	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-162	8	7
β-strand	171-176	6	8
α-helix	183	1
β-strand	184-188	5	8

Chain C: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-10	3
α-helix	14-16	3
β-strand	17	1	9
α-helix	22-28	7
β-strand	33-39	7	10
β-strand	42	1	11
β-strand	48-52	5	11
β-strand	63-67	5	11
α-helix	71-77	7
β-strand	81-86	6	10
β-strand	89	1	11
β-strand	112-115	4	11
β-strand	118-120	3	10
β-strand	125-138	14	12
β-strand	141-152	12	12
β-strand	154-156	3	13
α-helix	157-171	15
β-strand	182-191	10	12
β-strand	194-199	6	12
α-helix	202-203	2
β-strand	205	1	9
α-helix	210-214	5
α-helix	215-219	5
β-strand	222-224	3	13
β-strand	229-236	8	12

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)
Dipeptide mimetic inhibitor	D	protein	6

Sequence of entity 1 (A), FASTA

>1D5X_1 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B), FASTA

>1D5X_2 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN (chains B)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN
GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSL
TSPLTVEWRARS

Sequence of entity 3 (C), FASTA

>1D5X_3 ENTEROTOXIN TYPE B (chains C)
ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGN
YDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTE
HNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNS
PYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

Sequence of entity 4 (D), FASTA

>1D5X_4 DIPEPTIDE MIMETIC INHIBITOR (chains D)
XARAXS

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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