9QWK: S2c-a5b6 TCR

Crystal structure of S2c-a5b6 TCR in complex with CD1c. Determined by X-ray diffraction at 2.27 Å resolution. Released 20 Aug 2025.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Homo sapiens
Chains: 16
Atoms: 26,177
Mol. weight: 603.81 kDa
Ligands: D10, NAG, FUC
Released: 20 Aug 2025

Explore 9QWK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QWK contains 108 α-helices and 302 β-strands across 16 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	1
β-strand	24-32	9	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-85	26
α-helix	89-91	3
β-strand	94-103	10	1
α-helix	109-110	2
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	135-137	3
α-helix	138-151	14
α-helix	153-161	9
α-helix	162-166	5
α-helix	167-182	16
β-strand	186	1	2
α-helix	187-188	2
β-strand	189-195	7	3
β-strand	204-212	9	3
β-strand	213	1	2
β-strand	218	1	4
β-strand	221	1	5
β-strand	222-223	2	6
β-strand	226-227	2	6
β-strand	232-233	2	3
β-strand	237-238	2	3
β-strand	244-251	8	3
β-strand	262-264	3	5
β-strand	265	1	4
α-helix	267-269	3
β-strand	274-276	3	5

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	7
α-helix	4-5	2
β-strand	6-11	6	8
β-strand	21-30	10	8
β-strand	31	1	7
β-strand	35-41	7	9
β-strand	44-45	2	9
β-strand	50-51	2	8
α-helix	52-54	3
β-strand	55-56	2	8
β-strand	62-70	9	8
β-strand	78-84	7	9
β-strand	91-94	4	9
β-strand	101	1	8

Chain D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	10
β-strand	11-14	4	11
β-strand	19-21	3	12
β-strand	23-25	3	10
β-strand	32-38	7	11
β-strand	45-50	6	11
α-helix	55	1
β-strand	56-59	4	12
β-strand	62-65	4	12
β-strand	67	1	10
β-strand	72	1	10
β-strand	75-77	3	12
α-helix	82-84	3
β-strand	86-93	8	11
α-helix	95-97	3
α-helix	100	1
β-strand	101-103	3	11
β-strand	107-112	6	11
α-helix	113	1
β-strand	121-126	6	13
β-strand	127	1	14
β-strand	134-139	6	13
α-helix	148-150	3
β-strand	155-157	3	13
α-helix	158-160	3
β-strand	161-165	5	13
α-helix	166-168	3
β-strand	170-179	10	13
α-helix	186-189	4

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	10-14	5	16
β-strand	19-24	6	15
β-strand	31-37	7	16
β-strand	44-50	7	16
β-strand	53-57	5	16
β-strand	65-68	4	15
β-strand	75-79	5	15
α-helix	84-86	3
β-strand	88-95	8	16
α-helix	102-104	3
β-strand	105-106	2	16
β-strand	110-115	6	16
α-helix	118-120	3
β-strand	122	1	17
α-helix	123-124	2
β-strand	125-129	5	14
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	14
β-strand	152	1	17
β-strand	156-162	7	18
β-strand	165-167	3	18
β-strand	171-173	3	14
β-strand	178-179	2	14
β-strand	189-198	10	14
α-helix	199-203	5
β-strand	208-215	8	18
β-strand	218	1	19
α-helix	229-230	2
β-strand	232	1	19
β-strand	234-241	8	18

Chain F: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	123-125	3	20
β-strand	128-132	5	21
β-strand	137-142	6	20
β-strand	149-155	7	21
β-strand	162-168	7	21
β-strand	171-175	5	21
β-strand	183-186	4	20
β-strand	193-197	5	20
α-helix	202-204	3
β-strand	207-213	7	21
α-helix	220-222	3
β-strand	223-224	2	21
β-strand	228-233	6	21
α-helix	236-238	3
β-strand	240	1	22
α-helix	241-242	2
β-strand	243-247	5	23
α-helix	248-250	3
α-helix	251-257	7
β-strand	259-269	11	23
β-strand	270	1	22
β-strand	274-280	7	24
β-strand	283-285	3	24
β-strand	289-291	3	23
β-strand	296-297	2	23
β-strand	307-316	10	23
α-helix	317-321	5
β-strand	326-333	8	24
β-strand	336	1	25
α-helix	347-348	2
β-strand	350	1	25
β-strand	352-359	8	24

Chain G: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	26
β-strand	24-32	9	26
β-strand	35-41	7	26
β-strand	46-49	4	26
α-helix	60-85	26
β-strand	94-105	12	26
β-strand	108-118	11	26
β-strand	121-127	7	26
β-strand	130-133	4	26
α-helix	135-137	3
α-helix	138-151	14
α-helix	153-161	9
α-helix	162-166	5
α-helix	167-177	11
α-helix	179-182	4
β-strand	186	1	27
α-helix	187-188	2
β-strand	189-195	7	28
β-strand	203-212	10	28
β-strand	213	1	27
β-strand	218-223	6	29
β-strand	226-227	2	29
β-strand	232-233	2	28
β-strand	237-238	2	28
β-strand	244-252	9	28
β-strand	260-265	6	29
α-helix	267-269	3
β-strand	274-276	3	29

Chain H: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	30
β-strand	12-15	4	31
β-strand	20-22	3	32
β-strand	24-26	3	30
β-strand	33-39	7	31
β-strand	46-51	6	31
α-helix	56	1
β-strand	57-60	4	32
β-strand	63-66	4	32
β-strand	68	1	30
β-strand	73	1	30
β-strand	76-78	3	32
α-helix	83-85	3
β-strand	87-94	8	31
α-helix	96-98	3
α-helix	101	1
β-strand	102-104	3	31
β-strand	108-113	6	31
α-helix	114	1
β-strand	122-127	6	33
β-strand	128	1	23
β-strand	135-140	6	33
α-helix	149-151	3
β-strand	156-158	3	33
α-helix	159-161	3
β-strand	162-166	5	33
α-helix	167-169	3
β-strand	171-180	10	33
α-helix	187-190	4

Chains J, O and T: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	34
α-helix	4-5	2
β-strand	6-11	6	35
β-strand	21-30	10	35
β-strand	31	1	34
β-strand	36-41	6	36
β-strand	44-45	2	36
β-strand	50-51	2	35
α-helix	52-54	3
β-strand	55-56	2	35
β-strand	62-70	9	35
β-strand	78-83	6	36
β-strand	91-94	4	36
β-strand	101	1	35

6 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
Beta-2-microglobulin,T-cell surface glycoprotein CD1c	A, B, G, J, L, O, Q, T	protein	442	Homo sapiens	P29017 (AlphaFold model), P61769 (AlphaFold model)
TCR alpha	D, H, M, R	protein	200	Homo sapiens
TCR beta	E, F, K, P	protein	246	Homo sapiens

Sequence of entity 1 (A, B, G, J, L, O, Q, T), FASTA

>9QWK_1 Beta-2-microglobulin,T-cell surface glycoprotein CD1c (chains A, B, G, J, L, O, Q, T)
MYRMQLLSCIALSLALVTNSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLL
KNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDIG
GGGSGGGGSGGGGSEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLH
NWSKGNFSNEELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPE
GFFQVAFNGLDLLSFQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFL
LGLLDAGKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWMRNEQEQLGT
KHGDILPNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGSLSTPPTPSTPP
TGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (D, H, M, R), FASTA

>9QWK_2 TCR alpha (chains D, H, M, R)
MGNSVTQMEGPVTLSEEAFLTINCTYTAYGLYSLFWYVQYPGEGLQLLLKATKADDKGSN
KGFEATYRKETTSFHLEKGSVQVSDSAVYFCALSGQYGWGKLQFGAGTQVVVTPDIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTQVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
QKSDFACANAFQNSIIPEDT

Sequence of entity 3 (E, F, K, P), FASTA

>9QWK_3 TCR beta (chains E, F, K, P)
MDTGVSQNPRHKITKRGQNVTFRCDPISEHSRLYWYRQTLGQGPEFLTYFQNEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSPRMVRGAEAFFGQGTRLTVVEDLN
KVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALQDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
D10	Decane	C10 H22	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
FUC	alpha-L-fucopyranose	C6 H12 O5	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

A CD1c lipid agnostic T cell receptor bispecific engager redirects T cells against CD1c + cells. Szoke-Kovacs, R., Khakoo, S., Rangel, V.L. et al. Front Immunol (2025) 16:1614610-1614610. DOI 10.3389/fimmu.2025.1614610 · PubMed

Other PDB entries of the same protein (UniProt P29017 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MX4 1.73 Å, CD1c with antigen analogue 1
7MXF 2.0 Å, CD1c with antigen analogue 2
9QWJ 2.04 Å, Crystal structure of S2c TCR in complex with CD1c
7MXH 2.11 Å, CD1c with antigen analogue 3
5C9J 2.4 Å, Human CD1c with ligands in A' and F' channel
3OV6 2.5 Å, CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide)
4ONO 2.71 Å, CD1c in complex with PM (phosphomycoketide)
6C09 2.95 Å, Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex
6C15 3.21 Å, CD1c in complex with phosphatidylcholine

Browse structure collections

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