5KSU: HLA-DQ2.5-CLIP1 at 2.73 resolution

Crystal structure of HLA-DQ2.5-CLIP1 at 2.73 resolution. Determined by X-ray diffraction at 2.73 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 2.73 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,139
Mol. weight: 95.77 kDa
Released: 5 Apr 2017

Explore 5KSU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KSU contains 26 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
α-helix	36-38	3
β-strand	40-43	4	1
α-helix	46-50	5
β-strand	52	1	2
α-helix	56-76	21
α-helix	81-87	7
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-71	7
α-helix	74	1
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	5
β-strand	98-103	6	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
α-helix	145-147	3
β-strand	148-149	2	6
β-strand	155-162	8	6
β-strand	170-176	7	7
β-strand	184-189	6	7

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	-1	1	2

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	8
β-strand	19-26	8	8
β-strand	29-35	7	8
β-strand	40-43	4	8
α-helix	46-48	3
β-strand	52	1	9
α-helix	57-76	20
α-helix	81-87	7
β-strand	88-93	6	10
β-strand	103-112	10	10
β-strand	118-123	6	11
β-strand	126-127	2	11
β-strand	132-134	3	10
α-helix	137	1
β-strand	138-139	2	10
β-strand	145-153	9	10
β-strand	156	1	12
β-strand	159	1	12
β-strand	161-166	6	11
β-strand	174-178	5	11

Chain E: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	8
β-strand	23-32	10	8
β-strand	35-41	7	8
β-strand	47-49	3	8
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	13
β-strand	98-103	6	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
α-helix	145-147	3
β-strand	148-149	2	14
β-strand	155-162	8	14
α-helix	165-166	2
β-strand	171-176	6	15
β-strand	184-188	5	15

Chain F: 1 helix, 1 β-strand

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, D	protein	199	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B, E	protein	204	Homo sapiens	Q5Y7D3 (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

>5KSU_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, D)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPEIPAPMSELTEVDIEGR

Sequence of entity 2 (B, E), FASTA

>5KSU_2 MHC class II HLA-DQ-beta-1 (chains B, E)
RDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEY
WNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QSPITVEWRAQSESAQSKVDIEGR

Sequence of entity 3 (C, F), FASTA

>5KSU_3 HLA class II histocompatibility antigen gamma chain (chains C, F)
PVSKMRMATPLLMQA

Primary citation

Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides. Nguyen, T.B., Jayaraman, P., Bergseng, E. et al. J Biol Chem (2017) 292:9218-9228. DOI 10.1074/jbc.M117.785139 · PubMed

Other PDB entries of the same protein (UniProt P01909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6U3M 1.9 Å, DQ2-P.fluor-alpha1a
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
6MFG 2.0 Å, HLA-DQ2-glia-alpha1
2NNA 2.1 Å, Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
8W84 2.1 Å, HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02
5KSV 2.19 Å, Crystal structure of HLA-DQ2.5-CLIP2
9EJG 2.2 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
1S9V 2.22 Å, Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
8W86 2.24 Å, HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
1JK8 2.4 Å, Crystal structure of a human insulin peptide-HLA-DQ8 complex
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2

Browse structure collections

About this viewer

MolViewer shows 5KSU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.