6DKP: PDB entry 6DKP

The complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, human Class I MHC HLA-A2 and MART-1(26-35)(A27L) peptide. Determined by X-ray diffraction at 2.97 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 2.97 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,539
Mol. weight: 94.08 kDa
Released: 10 Apr 2019

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

Secondary structure: helices and β-sheets

6DKP contains 22 α-helices and 75 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
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	140-149	10
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-173	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain D: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	10-13	4	9
β-strand	18-24	7	8
β-strand	32-37	6	9
α-helix	42-43	2
β-strand	44-49	6	9
β-strand	53-57	5	8
β-strand	60-65	6	8
α-helix	66-68	3
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-91	8	9
β-strand	97-99	3	9
β-strand	103-108	6	9
α-helix	109-111	3
β-strand	117-121	5	10
β-strand	122	1	11
β-strand	130-135	6	10
β-strand	152-153	2	10
β-strand	157-160	4	10
α-helix	162-164	3
β-strand	167-175	9	10
β-strand	196	1	10

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	12
β-strand	13-17	5	13
β-strand	22-24	3	14
β-strand	25-28	4	12
β-strand	34-40	7	13
β-strand	46-52	7	13
β-strand	59-60	2	13
β-strand	67-69	3	14
β-strand	76	1	12
β-strand	79-81	3	14
α-helix	86-88	3
β-strand	90-97	8	13
β-strand	105-106	2	13
β-strand	110-115	6	13
α-helix	118-120	3
β-strand	122	1	15
β-strand	125-129	5	16
β-strand	130	1	11
α-helix	133-139	7
β-strand	141-151	11	16
β-strand	152	1	15
β-strand	156-162	7	17
β-strand	165-167	3	17
β-strand	171-173	3	16
β-strand	178-179	2	16
β-strand	189-198	10	16
α-helix	199-203	5
β-strand	208-215	8	17
β-strand	218	1	18
β-strand	232	1	18
β-strand	234-241	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma antigen recognized by T-cells 1	C	protein	10	Homo sapiens	Q16655 (AlphaFold model)
DMF5 T-cell Receptor Alpha Chain fusion	D	protein	200	Homo sapiens	A0A075B6T6 (AlphaFold model), P01848
DMF5 T-cell Receptor Beta Chain fusion	E	protein	243	Homo sapiens	A0A1B0GXE1, K7N5M4

Sequence of entity 1 (A), FASTA

>6DKP_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>6DKP_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6DKP_3 Melanoma antigen recognized by T-cells 1 (chains C)
ELAGIGILTV

Sequence of entity 4 (D), FASTA

>6DKP_4 DMF5 T-cell Receptor Alpha Chain fusion (chains D)
MKEVEQNSGPLSVPEGAIASLNCTYSYRGSQSFFWYRQYSGKSPELIMFIASNGDKEDGR
FTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>6DKP_5 DMF5 T-cell Receptor Beta Chain fusion (chains E)
MIAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGE
VPDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSWSFGTEAFFGQGTRLTVVEDLNKVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design. Hellman, L.M., Foley, K.C., Singh, N.K. et al. Mol Ther (2019) 27:300-313. DOI 10.1016/j.ymthe.2018.12.010 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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