2P5E: High Affinity Human T-Cell Receptors

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry. Determined by X-ray diffraction at 1.89 Å resolution. Released 25 Sept 2007.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,474
Mol. weight: 95.06 kDa
Ligands: IPA, MG
Released: 25 Sept 2007

Explore 2P5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2P5E contains 27 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: 11 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	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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
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	222-224	3	4
β-strand	228-230	3	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	270-273	4	4

Chain B: 3 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
α-helix	46	1
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: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	30-38	9	9
β-strand	44-50	7	9
β-strand	51	1	10
β-strand	54	1	10
β-strand	56-59	4	8
β-strand	62-66	5	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	103-104	2	9
β-strand	108-113	6	9
β-strand	122-128	7	11
β-strand	135-140	6	11
α-helix	148-150	3
β-strand	153	1	11
β-strand	156-158	3	11
α-helix	159-161	3
β-strand	162-166	5	11
α-helix	167-169	3
β-strand	171-180	10	11
α-helix	187-189	3

Chain E: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	8-12	5	13
β-strand	17-19	3	14
β-strand	20-23	4	12
β-strand	29-35	7	13
β-strand	42-49	8	13
β-strand	52-55	4	13
β-strand	62-64	3	14
β-strand	71	1	12
β-strand	74-76	3	14
α-helix	81-83	3
β-strand	85-92	8	13
β-strand	101-102	2	13
β-strand	106-111	6	13
α-helix	114-116	3
β-strand	118	1	15
α-helix	119-120	2
β-strand	121-126	6	11
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	11
β-strand	148	1	15
β-strand	152-158	7	16
β-strand	161-163	3	16
β-strand	167-169	3	11
α-helix	173	1
β-strand	174-175	2	11
β-strand	185-194	10	11
α-helix	195-199	5
β-strand	204-211	8	16
β-strand	214	1	17
α-helix	225-226	2
β-strand	228	1	17
β-strand	230-237	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Cancer/testis antigen 1B	C	protein	9		P78358 (AlphaFold model)
T-Cell Receptor, Alpha Chain	D	protein	195	Homo sapiens	A0A0B4J279 (AlphaFold model)
Hypothetical protein	E	protein	242	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>2P5E_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>2P5E_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPCIVKWDRDM

Sequence of entity 3 (C), FASTA

>2P5E_3 Cancer/testis antigen 1B (chains C)
SLLMWITQC

Sequence of entity 4 (D), FASTA

>2P5E_4 T-Cell Receptor, Alpha Chain (chains D)
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLITPWQREQTS
GRLNASLDKSSGSSTLYIAASQPGDSATYLCAVRPLLDGTYIPTFGRGTSLIVHPYIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNS

Sequence of entity 5 (E), FASTA

>2P5E_5 Hypothetical protein (chains E)
GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVAIQTTDQGEVPN
GYNVSRSTIEDFPLRLLSAAPSQTSVYFCASSYLGNTGELFFGEGSRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
DA

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4, GOL, EPE) are not listed.

Primary citation

Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry. Sami, M., Rizkallah, P.J., Dunn, S. et al. Protein Eng Des Sel (2007) 20:397-403. DOI 10.1093/protein/gzm033 · PubMed

Other PDB entries of the same protein (UniProt A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
7QPJ 1.54 Å, Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10…
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
7MKB 1.9 Å, Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL
7U21 1.9 Å, Human Class I MHC HLA-A2 in complex with AVGSYVYSV peptide

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