6APN: PDB entry 6APN

HLA-A*0201 single chain trimer with HPV.16 E7 peptide LLMGTLGIV. Determined by X-ray diffraction at 2.22 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 2.22 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,256
Mol. weight: 100.18 kDa
Released: 22 Aug 2018

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

Secondary structure: helices and β-sheets

6APN contains 30 α-helices and 60 β-strands across 2 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: 15 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	27	1	1
α-helix	28-29	2
β-strand	30-35	6	2
β-strand	45-54	10	2
β-strand	55	1	1
β-strand	60-65	6	3
β-strand	68-69	2	3
α-helix	70	1
β-strand	74-75	2	2
α-helix	76-78	3
β-strand	79-80	2	2
β-strand	86-94	9	2
β-strand	102-107	6	3
β-strand	115-118	4	3
β-strand	146-155	10	4
α-helix	163	1
β-strand	164-171	8	4
β-strand	174-180	7	4
β-strand	189-190	2	4
α-helix	193-197	5
α-helix	200-227	28
β-strand	237-246	10	4
β-strand	252-261	10	4
β-strand	264-269	6	4
β-strand	276-278	3	4
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	5
α-helix	327-328	2
β-strand	329-335	7	6
β-strand	341-351	11	6
β-strand	352	1	5
β-strand	357-362	6	7
β-strand	365-367	3	7
β-strand	372-373	2	6
α-helix	374-376	3
β-strand	377-378	2	6
β-strand	384-393	10	6
α-helix	397-399	3
β-strand	400-405	6	7
β-strand	413-415	3	7

Chain B: 15 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	27	1	8
α-helix	28-29	2
β-strand	30-35	6	9
β-strand	45-54	10	9
β-strand	55	1	8
β-strand	60-65	6	10
β-strand	68-69	2	10
α-helix	70	1
β-strand	74-75	2	9
β-strand	79-80	2	9
β-strand	86-94	9	9
β-strand	102-107	6	10
β-strand	115-118	4	10
α-helix	119-120	2
β-strand	146-155	10	11
α-helix	163	1
β-strand	164-171	8	11
β-strand	174-180	7	11
β-strand	189-190	2	11
α-helix	193-196	4
α-helix	200-227	28
β-strand	237-246	10	11
β-strand	252-261	10	11
β-strand	264-269	6	11
β-strand	276-278	3	11
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	12
α-helix	327-328	2
β-strand	329-335	7	13
β-strand	341-351	11	13
β-strand	352	1	12
β-strand	357-362	6	14
β-strand	365-366	2	14
β-strand	371-373	3	13
α-helix	374-376	3
β-strand	377-378	2	13
β-strand	384-393	10	13
α-helix	397-399	3
β-strand	400-405	6	14
β-strand	413-416	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera	A, B	protein	446	Homo sapiens	P03129 (AlphaFold model), P04439 (AlphaFold model), P61769 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6APN_1 Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera (chains A, B)
LLMGTLGIVGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIE
VDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD
RDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFD
SDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGAYNQSEAGSHTVQR
MYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLR
AYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTW
QRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEEN
LYFQGHHHHHHGLNDIFEAQKIEWHE

Primary citation

Effects of HLA single chain trimer design on peptide presentation and stability. Finton, K.A.K. To be published.

Other PDB entries of the same protein (UniProt P03129 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YOZ 2.25 Å, p107 pocket domain in complex with HPV E7 peptide
7SR3 2.49 Å, Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPETTDL
7SQP 2.53 Å, Single chain trimer HLA-A*02:01 (Y108C) with HPV.16 E7 peptide YMLDLQPETTDL
7SR0 2.54 Å, Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPET
7SR4 2.59 Å, Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPETTDLYC
7SSH 2.73 Å, Single chain trimer HLA-A*02:01 (Y108A) with HPV.16 E7 peptide YMLDLQPETTDLYC
7ST3 2.78 Å, Consequences of HLA single chain trimer mutations on peptide presentation and binding…
9Z51 3.13 Å, HPV_Jin TCR in complex with HLA-A*02:01 presenting HPV16 E7 9mer peptide (11-YMLDLQPET-19)
9UUK 3.2 Å, Crystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to…
9UUL 3.3 Å, Crystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to…
9UUJ 3.7 Å, Crystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to…

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