3PGD: PDB entry 3PGD

Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation. Determined by X-ray diffraction at 2.72 Å resolution. Released 8 Dec 2010.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,324
Mol. weight: 94.35 kDa
Released: 8 Dec 2010

Explore 3PGD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PGD contains 24 α-helices and 64 β-strands across 6 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, 16 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	46-48	3
β-strand	54	1	2
α-helix	56-76	21
α-helix	81-84	4
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	4
α-helix	137	1
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 5 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	46-49	4	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
β-strand	95	1	6
β-strand	98-104	7	7
β-strand	114-122	9	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-138	3	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-162	8	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	107	1	2
α-helix	108-110	3
α-helix	112-115	4

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	9
β-strand	19-26	8	9
β-strand	29-35	7	9
β-strand	40-43	4	9
α-helix	46-50	5
β-strand	54	1	10
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	11
α-helix	86-87	2
β-strand	88-93	6	12
β-strand	103-112	10	12
β-strand	113	1	11
β-strand	118-123	6	13
β-strand	126-128	3	13
β-strand	133-134	2	12
α-helix	137	1
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	160-166	7	13
β-strand	174-179	6	13

Chain E: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	9
β-strand	23-32	10	9
β-strand	35-41	7	9
β-strand	47-49	3	9
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
β-strand	95	1	14
β-strand	98-104	7	15
β-strand	114-122	9	15
β-strand	123	1	14
β-strand	128-133	6	16
β-strand	136-138	3	16
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	155-162	8	15
β-strand	170-176	7	16
β-strand	184-189	6	16

Chain F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	107	1	10
α-helix	108-110	3
α-helix	112-116	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	193	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, E	protein	199	Homo sapiens	P01911 (AlphaFold model)
HLA class II histocompatibility antigen gamma chain	C, F	protein	15	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3PGD_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGA
LANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNV
TWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWE
FDAPSPLPETTEN

Sequence of entity 2 (B, E), FASTA

>3PGD_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains B, E)
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAE
YWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSV
SGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPS
VTSPLTVEWRARSESAQSK

Sequence of entity 3 (C, F), FASTA

>3PGD_3 HLA class II histocompatibility antigen gamma chain (chains C, F)
KMRMATPLLMQALPM

Primary citation

Bidirectional binding of invariant chain peptides to an MHC class II molecule. Gunther, S., Schlundt, A., Sticht, J. et al. Proc Natl Acad Sci U S A (2010) 107:22219-22224. DOI 10.1073/pnas.1014708107 · 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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