1BX2: HLA-DR2

Crystal structure of HLA-DR2 (DRA*0101,DRB1*1501) complexed with a peptide from human myelin basic protein. Determined by X-ray diffraction at 2.6 Å resolution. Released 21 Oct 1998.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,282
Mol. weight: 90.62 kDa
Ligands: NAG
Released: 21 Oct 1998

Explore 1BX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BX2 contains 18 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: 3 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	46-49	4
β-strand	53	1	2
α-helix	56-77	22
α-helix	82-84	3
β-strand	85	1	3
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	126-127	2	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	161-166	6	5
β-strand	174-178	5	5

Chain B: 5 helices, 16 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
β-strand	51	1	6
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	7
β-strand	98-104	7	8
β-strand	113-122	10	8
β-strand	123	1	7
β-strand	128-133	6	9
β-strand	136-138	3	9
β-strand	142-144	3	8
β-strand	148-149	2	8
β-strand	155-163	9	8
β-strand	170-176	7	9
β-strand	184-189	6	9

Chains C and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	88	1	2

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	10
β-strand	19-26	8	10
β-strand	29-35	7	10
β-strand	40-43	4	10
α-helix	46-50	5
β-strand	53	1	11
α-helix	56-77	22
α-helix	82-84	3
β-strand	85	1	12
β-strand	88-93	6	13
β-strand	103-112	10	13
β-strand	113	1	12
β-strand	118-123	6	14
β-strand	126-128	3	14
β-strand	133-134	2	13
β-strand	138-139	2	13
β-strand	145-153	9	13
β-strand	161-166	6	14
β-strand	174-178	5	14

Chain E: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	10
β-strand	23-32	10	10
β-strand	35-41	7	10
β-strand	47-49	3	10
β-strand	51	1	6
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	15
β-strand	98-104	7	16
β-strand	113-122	10	16
β-strand	123	1	15
β-strand	128-133	6	17
β-strand	136-137	2	17
α-helix	138	1
β-strand	142-144	3	16
β-strand	148-149	2	16
β-strand	155-163	9	16
β-strand	170-176	7	17
β-strand	184-189	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (HLA-DR2)	A, D	protein	180	Homo sapiens	P01903 (AlphaFold model)
Protein (HLA-DR2)	B, E	protein	191	Homo sapiens	P01911 (AlphaFold model)
Protein (HLA-DR2)	C, F	protein	15	Homo sapiens	P02686 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1BX2_1 PROTEIN (HLA-DR2) (chains A, D)
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALA
NIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTW
LRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

Sequence of entity 2 (B, E), FASTA

>1BX2_2 PROTEIN (HLA-DR2) (chains B, E)
TRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWN
SQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVSGF
YPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS
PLTVEWRARSE

Sequence of entity 3 (C, F), FASTA

>1BX2_3 PROTEIN (HLA-DR2) (chains C, F)
ENPVVHFFKNIVTPR

Ligands and cofactors

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

Primary citation

Crystal structure of HLA-DR2 (DRA*0101, DRB1*1501) complexed with a peptide from human myelin basic protein. Smith, K.J., Pyrdol, J., Gauthier, L. et al. J Exp Med (1998) 188:1511-1520. DOI 10.1084/jem.188.8.1511 · 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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