6ATZ: HLA-DRB1*1402

HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,247
Mol. weight: 88.71 kDa
Ligands: NAG, B3P
Released: 20 Sept 2017

Explore 6ATZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ATZ contains 28 α-helices and 62 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, 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	46-49	4
α-helix	56-76	21
α-helix	80-84	5
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	126-128	3	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: 8 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	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-85	5
α-helix	87-89	3
β-strand	95	1	5
β-strand	98-104	7	6
β-strand	114-122	9	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-138	3	7
β-strand	142-144	3	6
β-strand	148-149	2	6
β-strand	155-162	8	6
β-strand	170-176	7	7
α-helix	183	1
β-strand	184-189	6	7

Chain C: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	8
β-strand	19-26	8	8
β-strand	29-35	7	8
β-strand	40-43	4	8
α-helix	46-50	5
β-strand	53	1	9
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	10
α-helix	86-87	2
β-strand	88-93	6	11
β-strand	103-112	10	11
β-strand	113	1	10
β-strand	118-123	6	12
β-strand	126-128	3	12
β-strand	133-134	2	11
β-strand	138-139	2	11
β-strand	145-153	9	11
β-strand	161-166	6	12
β-strand	174-178	5	12

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	8
β-strand	23-32	10	8
β-strand	35-41	7	8
β-strand	46-49	4	8
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	81-85	5
α-helix	87-89	3
β-strand	95	1	13
α-helix	96-97	2
β-strand	98-104	7	14
β-strand	114-122	9	14
β-strand	123	1	13
β-strand	128-133	6	15
β-strand	136-138	3	15
β-strand	142-144	3	14
β-strand	148-149	2	14
β-strand	155-162	8	14
β-strand	170-176	7	15
α-helix	183	1
β-strand	184-189	6	15

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1	1	9
α-helix	4-9	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, C	protein	177	Homo sapiens	P01903 (AlphaFold model)
MHC class II antigen	B, D	protein	188	Homo sapiens	A0A0A1I7H6 (AlphaFold model)
Fibrinogen beta chain	E, F	protein	12	Homo sapiens	P02675 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6ATZ_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, C)
EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANI
AVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLR
NGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF

Sequence of entity 2 (B, D), FASTA

>6ATZ_2 MHC class II antigen (chains B, D)
TRPRFLEYSTSECHFFNGTERVRFLERYFHNQEENVRFDSDVGEYRAVTELGRPDAEYWN
SQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGF
YPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS
PLTVEWRA

Sequence of entity 3 (E, F), FASTA

>6ATZ_3 Fibrinogen beta chain (chains E, F)
GGYRARPAKAAT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
B3P	2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-pr…	C11 H26 N2 O6	1

Primary citation

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis. Scally, S.W., Law, S.C., Ting, Y.T. et al. Ann Rheum Dis (2017) 76:1915-1923. DOI 10.1136/annrheumdis-2017-211300 · 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

Browse structure collections

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