2Q6W: PDB entry 2Q6W

The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia. Determined by X-ray diffraction at 2.25 Å resolution. Released 24 Jul 2007.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,530
Mol. weight: 89.12 kDa
Released: 24 Jul 2007

Explore 2Q6W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Q6W contains 28 α-helices and 66 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	48-51	4
β-strand	54	1	2
α-helix	56-76	21
α-helix	80-84	5
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
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
α-helix	173	1
β-strand	174-179	6	5

Chain B: 7 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	71-73	3
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
β-strand	113-122	10	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	155-163	9	7
β-strand	171-176	6	8
β-strand	184-188	5	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	25	1	2
α-helix	26-33	8

Chain D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	9
β-strand	19-26	8	9
β-strand	29-35	7	9
β-strand	40-43	4	9
α-helix	48-50	3
β-strand	54	1	10
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	11
α-helix	86-87	2
β-strand	88-93	6	12
β-strand	98	1	13
β-strand	101	1	13
β-strand	103-112	10	12
β-strand	113	1	11
β-strand	118-123	6	14
β-strand	126-128	3	14
β-strand	133-134	2	12
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	160-166	7	14
α-helix	173	1
β-strand	174-179	6	14

Chain E: 9 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	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	15
α-helix	96-97	2
β-strand	98-103	6	16
α-helix	107-108	2
β-strand	113-122	10	16
β-strand	123	1	15
β-strand	128-132	5	17
β-strand	137-138	2	17
β-strand	142-144	3	16
β-strand	148-149	2	16
β-strand	155-163	9	16
α-helix	165-166	2
β-strand	171-176	6	17
β-strand	184-188	5	17

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	25	1	10
α-helix	26-32	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB3-1 beta chain	B, E	protein	190	Homo sapiens	P79483 (AlphaFold model)
Integrin beta-3	C, F	protein	12	Homo sapiens	P05106 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>2Q6W_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DA

Sequence of entity 2 (B, E), FASTA

>2Q6W_2 HLA class II histocompatibility antigen, DRB3-1 beta chain (chains B, E)
GDTRPRFLELRKSECHFFNGTERVRYLDRYFHNQEEFLRFDSDVGEYRAVTELGRPVAES
WNSQKDLLEQKRGRVDNYCRHNYGVGESFTVQRRVHPQVTVYPAKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSALTVEWRA

Sequence of entity 3 (C, F), FASTA

>2Q6W_3 Integrin beta-3 (chains C, F)
AWRSDEALPLGS

Primary citation

Crystallographic Structure of the Human Leukocyte Antigen DRA, DRB3*0101: Models of a Directional Alloimmune Response and Autoimmunity. Parry, C.S., Gorski, J., Stern, L.J. J Mol Biol (2007) 371:435-446. DOI 10.1016/j.jmb.2007.05.025 · 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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