5NHT: Human 199.54-16 TCR

human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2. Determined by X-ray diffraction at 3.2 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,613
Mol. weight: 96.44 kDa
Ligands: SCN
Released: 16 May 2018

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

Secondary structure: helices and β-sheets

5NHT contains 15 α-helices and 82 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: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	9
β-strand	11-14	4	10
β-strand	19-25	7	9
β-strand	32-38	7	11
β-strand	45-50	6	11
β-strand	54-58	5	9
β-strand	61-66	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	86-92	7	11
β-strand	99-100	2	11
α-helix	101	1
β-strand	104-105	2	11
β-strand	106-109	4	10
β-strand	118-121	4	12
β-strand	124	1	13
β-strand	132	1	14
β-strand	133-138	6	12
β-strand	152-154	3	14
β-strand	161	1	15
β-strand	168	1	15
β-strand	170-172	3	12
β-strand	174-176	3	14
α-helix	185-187	3
β-strand	197	1	12

Chain B: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
β-strand	10-12	3	17
β-strand	19-21	3	18
β-strand	23-25	3	16
β-strand	31-37	7	17
β-strand	43-49	7	17
β-strand	56-57	2	17
β-strand	65-66	2	18
β-strand	73	1	16
β-strand	76-78	3	18
β-strand	87-94	8	17
β-strand	104-105	2	17
β-strand	109-112	4	17
β-strand	121	1	19
β-strand	124	1	20
β-strand	127-128	2	13
α-helix	132-137	6
β-strand	140-145	6	13
β-strand	148-150	3	20
β-strand	151	1	19
β-strand	158-160	3	21
β-strand	165-166	2	21
β-strand	170-171	2	13
β-strand	178	1	20
β-strand	188-189	2	20
β-strand	192-197	6	13
α-helix	198-201	4
β-strand	208-212	5	21
β-strand	217	1	22
β-strand	231	1	22
β-strand	235-239	5	21

Chain H: 10 helices, 18 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
α-helix	45	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	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	183-185	3
β-strand	186	1	2
β-strand	189-193	5	3
β-strand	198-208	11	3
β-strand	216-219	4	4
β-strand	222-224	3	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	258-260	3	4
β-strand	271-272	2	4

Chain L: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	16	1	7
β-strand	19	1	7
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	8
β-strand	44-45	2	8
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	8
β-strand	91-94	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	H	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	L	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma antigen recognized by T-cells 1	P	protein	10	Homo sapiens	Q16655 (AlphaFold model)
T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain	A	protein	211	Homo sapiens	A0A075B6T6 (AlphaFold model), K7N5N2
T-cell receptor beta variable 19,TRB protein	B	protein	251	Homo sapiens	A0A0C4ZKA8, A0A5B3

Sequence of entity 1 (H), FASTA

>5NHT_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains H)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (L), FASTA

>5NHT_2 Beta-2-microglobulin (chains L)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P), FASTA

>5NHT_3 Melanoma antigen recognized by T-cells 1 (chains P)
ELAGIGILTV

Sequence of entity 4 (A), FASTA

>5NHT_4 T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain (chains A)
MQQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKED
GRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVGGGADGLTFGKGTHLIIQPYIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPENDGGGCK

Sequence of entity 5 (B), FASTA

>5NHT_5 T-cell receptor beta variable 19,TRB protein (chains B)
MGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIA
EGYSVSREKKESFPLTVTSAQKNPTAFYLCASSQGLAGAGELFFGEGSRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RADQDRGGGCD

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	1

Water and common crystallization additives (CL, K) are not listed.

Primary citation

human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2. Exertier, C., Reiser, J.-B., Housset, D. To be published.

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

Browse structure collections

About this viewer

MolViewer shows 5NHT 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.