1PYW: Human class II MHC protein HLA-DR1

Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza virus hemagglutinin, FVKQNA(MAA)AL, in complex with staphylococcal enterotoxin C3 variant 3B2 (SEC3-3B2). Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Dec 2003.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
Chains: 4
Atoms: 5,396
Mol. weight: 71.96 kDa
Released: 9 Dec 2003

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

Secondary structure: helices and β-sheets

1PYW contains 22 α-helices and 49 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	48-51	4
α-helix	56-76	21
α-helix	81-84	4
β-strand	85	1	2
α-helix	86-87	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	126-127	2	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	160-166	7	4
β-strand	174-179	6	4

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-31	9	1
β-strand	36-41	6	1
β-strand	47-49	3	1
α-helix	52-54	3
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	5
α-helix	96-97	2
β-strand	98-103	6	6
β-strand	113-122	10	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	155-163	9	6
β-strand	170-176	7	7
β-strand	184-189	6	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6

Chain D: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
α-helix	8-10	3
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	63-67	5	10
α-helix	71-78	8
β-strand	82-86	5	9
β-strand	89	1	10
β-strand	108-112	5	10
β-strand	115-117	3	9
β-strand	122	1	11
β-strand	129-137	9	12
β-strand	140-149	10	12
β-strand	151	1	11
β-strand	153-155	3	13
α-helix	156-171	16
β-strand	183-189	7	12
β-strand	195-199	5	12
α-helix	202-203	2
β-strand	205	1	8
α-helix	210-214	5
α-helix	215-219	5
β-strand	222-224	3	13
β-strand	229-235	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DR-1 beta chain	B	protein	190	Homo sapiens	P01911 (AlphaFold model)
9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL	C	protein	10		P03437
Enterotoxin type C-3	D	protein	239	Staphylococcus aureus subsp. aureus Mu50	P0A0L3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1PYW_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DA

Sequence of entity 2 (B), FASTA

>1PYW_2 HLA class II histocompatibility antigen, DR-1 beta chain (chains B)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C), FASTA

>1PYW_3 9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL (chains C)
XFVKQNAAAL

Sequence of entity 4 (D), FASTA

>1PYW_4 Enterotoxin type C-3 (chains D)
ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKN
YDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEG
NHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSP
YETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG

Primary citation

Exploration of the P6/P7 region of the peptide-binding site of the human class II Major Histocompatability Complex Protein HLA-DR1. Zavala-Ruiz, Z., Sundberg, E.J., Stone, J.D. et al. J Biol Chem (2003) 278:44904-44912. DOI 10.1074/jbc.M307652200 · 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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