1D9K: Complex between D10 TCR and pmhc I-ak/ca

Crystal structure of complex between D10 TCR and pmhc I-ak/ca. Determined by X-ray diffraction at 3.2 Å resolution. Released 15 Dec 1999.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Mus musculus
Chains: 10
Atoms: 9,962
Mol. weight: 141.23 kDa
Ligands: NAG
Released: 15 Dec 1999

Explore 1D9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D9K contains 28 α-helices and 134 β-strands across 10 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: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	10-13	4	2
α-helix	17	1
β-strand	18-24	7	1
β-strand	32	1	3
β-strand	34-36	3	4
β-strand	44-45	2	4
β-strand	49	1	3
β-strand	55-58	4	1
β-strand	61-67	7	1
β-strand	72-77	6	1
β-strand	86	1	2
β-strand	89-90	2	4
β-strand	91-92	2	5
β-strand	105-106	2	5
β-strand	112-115	4	2

Chain B: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	32	1	8
β-strand	35-37	3	7
β-strand	38	1	9
β-strand	41	1	9
β-strand	45	1	7
β-strand	48	1	10
β-strand	49	1	8
β-strand	56	1	10
β-strand	66-71	6	6
β-strand	73-79	7	6
α-helix	84-86	3
β-strand	89-91	3	7
β-strand	93-94	2	8
α-helix	98-104	3
β-strand	107-108	2	8
β-strand	112-116	5	7

Chain C: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	12	11
β-strand	19-26	8	11
β-strand	29-35	7	11
β-strand	40-43	4	11
α-helix	48-51	4
β-strand	53-54	2	12
α-helix	56-76	21
α-helix	81-84	4
β-strand	88	1	13
β-strand	91-93	3	14
β-strand	103-112	10	14
β-strand	118-123	6	15
β-strand	127-128	2	15
β-strand	132-134	3	14
α-helix	136-137	2
β-strand	138-139	2	14
β-strand	145-153	9	14
β-strand	161-166	6	15
β-strand	174-178	5	15

Chain D: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	11
α-helix	20-22	3
β-strand	23-32	10	11
β-strand	35-41	7	11
β-strand	46-48	3	11
α-helix	52-54	3
α-helix	55-62	8
α-helix	68-74	7
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-86	5
β-strand	95	1	16
β-strand	98-99	2	17
β-strand	113-116	4	18
β-strand	119-122	4	17
β-strand	123	1	16
β-strand	128-133	6	19
β-strand	136-138	3	19
β-strand	142	1	18
β-strand	148-149	2	17
β-strand	155-157	3	17
β-strand	160-163	4	18
β-strand	171-176	6	19
β-strand	184-187	4	19

Chain E: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	20
β-strand	10-13	4	2
β-strand	15	1	21
β-strand	18-24	7	20
β-strand	31-37	7	2
β-strand	43-50	8	2
β-strand	55-58	4	20
β-strand	62-67	6	20
α-helix	68-70	3
β-strand	72-77	6	20
β-strand	80	1	21
β-strand	86-90	5	2
β-strand	91-92	2	22
β-strand	93	1	2
β-strand	105-106	2	22
β-strand	110-115	6	2

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	23
β-strand	10-13	4	24
β-strand	20-25	6	23
β-strand	31-34	4	25
β-strand	37	1	24
β-strand	47-49	3	25
β-strand	56-57	2	25
β-strand	66-71	6	23
β-strand	73-78	6	23
α-helix	84-86	3
β-strand	89-90	2	24
β-strand	92-95	4	25
β-strand	107-108	2	25
α-helix	109	1
β-strand	112-116	5	24

Chain G: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	26
β-strand	12-15	4	26
β-strand	19-21	3	26
β-strand	23-26	4	26
β-strand	29-35	7	26
β-strand	40-43	4	26
α-helix	46-48	3
β-strand	53-54	2	27
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	28
β-strand	88	1	29
β-strand	91-93	3	30
β-strand	103-107	5	30
β-strand	109-112	4	31
β-strand	113	1	28
β-strand	120-122	3	32
β-strand	127	1	32
β-strand	132-134	3	30
β-strand	138-139	2	31
β-strand	145-147	3	31
β-strand	149-153	5	30
β-strand	161-164	4	32
β-strand	176-178	3	32

Chain H: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	26
α-helix	20-22	3
β-strand	24-32	9	26
β-strand	35-41	7	26
β-strand	46-48	3	26
α-helix	55-62	8
α-helix	69-74	6
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-86	5
β-strand	95	1	33
β-strand	98-99	2	34
β-strand	102-103	2	35
β-strand	113-116	4	35
β-strand	119-120	2	34
β-strand	123	1	33
β-strand	128-132	5	36
β-strand	137	1	36
β-strand	142-144	3	35
α-helix	145-147	3
β-strand	148-149	2	37
β-strand	155-156	2	37
β-strand	157	1	34
β-strand	159-163	5	35
β-strand	172-176	5	36
β-strand	184-187	4	36

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell receptor D10 (alpha chain)	A, E	protein	110	Mus musculus	P01739 (AlphaFold model)
T-cell receptor D10 (beta chain)	B, F	protein	112	Mus musculus	P04213 (AlphaFold model)
MHC I-ak a chain (alpha chain)	C, G	protein	183	Mus musculus	P01910 (AlphaFold model)
MHC I-ak B chain (beta chain)	D, H	protein	188	Mus musculus	P06343 (AlphaFold model)
Conalbumin peptide	P, Q	protein	16	Mus musculus	P02789

Sequence of entity 1 (A, E), FASTA

>1D9K_1 T-CELL RECEPTOR D10 (ALPHA CHAIN) (chains A, E)
QVRQSPQSLTVWEGETTILNCSYEDSTFDYFPWYRQFPGKSPALLIAISLVSNKKEDGRF
TIFFNKREKKLSLHITDSQPGDSATYFCAATGSFNKLTFGAGTRLAVSPY

Sequence of entity 2 (B, F), FASTA

>1D9K_2 T-CELL RECEPTOR D10 (BETA CHAIN) (chains B, F)
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQENFSLILELATPSQTSVYFCASGGQGRAEQFFGPGTRLTVLGS

Sequence of entity 3 (C, G), FASTA

>1D9K_3 MHC I-AK A CHAIN (ALPHA CHAIN) (chains C, G)
IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLRRFEPQGG
LQNIATGKHNLEILTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE
PEI

Sequence of entity 4 (D, H), FASTA

>1D9K_4 MHC I-AK B CHAIN (BETA CHAIN) (chains D, H)
GSERHFVHQFQPFCYFTNGTQRIRLVIRYIYNREEYVRFDSDVGEYRAVTELGRPDAEYW
NKQYLERTRAELDTVCRHNYEKTETPTSLRRLEQPSVVISLSRTEALNHHNTLVCSVTDF
YPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKS
PITVEWRA

Sequence of entity 5 (P, Q), FASTA

>1D9K_5 CONALBUMIN PEPTIDE (chains P, Q)
GNSHRGAIEWEGIESG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

The crystal structure of a T cell receptor in complex with peptide and MHC class II. Reinherz, E.L., Tan, K., Tang, L. et al. Science (1999) 286:1913-1921. DOI 10.1126/science.286.5446.1913 · PubMed

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