5U98: PDB entry 5U98

The crystal structure of a self-peptide complexed to Abacavir and HLA-B*57:01. Determined by X-ray diffraction at 2.0 Å resolution. Released 19 Jul 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,152
Mol. weight: 89.81 kDa
Ligands: 1KX
Released: 19 Jul 2017

Explore 5U98 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U98 contains 29 α-helices and 60 β-strands across 4 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
α-helix	225-227	3
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, B-57 alpha chain	A, D	protein	277	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Homo sapiens	P61769 (AlphaFold model)
Val-thr-thr-asp-ile-gln-val-lys-val	C, F	protein	9	Homo sapiens	O00267 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5U98_1 HLA class I histocompatibility antigen, B-57 alpha chain (chains A, D)
MGSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEY
WDGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHDQSAYD
GKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETL
QRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDR
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, E), FASTA

>5U98_2 Beta-2-microglobulin (chains B, E)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>5U98_3 VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL (chains C, F)
VTTDIQVKV

Ligands and cofactors

ID	Name	Formula	Copies
1KX	{(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}meth…	C14 H18 N6 O	2

Primary citation

Structural Elements Recognized by Abacavir-Induced T Cells. Yerly, D., Pompeu, Y.A., Schutte, R.J. et al. Int J Mol Sci (2017) 18. DOI 10.3390/ijms18071464 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

Browse structure collections

About this viewer

MolViewer shows 5U98 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.