9C9D: Protein receptor

Protein receptor. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Aug 2025.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,189
Mol. weight: 119.03 kDa
Ligands: 30W
Released: 27 Aug 2025

Explore 9C9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C9D contains 28 α-helices and 92 β-strands across 5 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	15-16	2
β-strand	22-28	7	1
β-strand	31-37	7	1
β-strand	44-45	2	1
α-helix	48-51	4
α-helix	56-84	29
β-strand	91-100	10	1
β-strand	106-114	9	1
β-strand	117-123	7	1
β-strand	128-131	4	1
α-helix	134-145	12
α-helix	147-155	9
α-helix	156-160	5
α-helix	161-171	11
α-helix	173-176	4
β-strand	180	1	2
β-strand	183-192	10	3
β-strand	195-205	11	3
β-strand	206	1	2
β-strand	211-216	6	4
α-helix	225	1
β-strand	226-227	2	3
β-strand	231-232	2	3
β-strand	238-246	9	3
β-strand	254-259	6	4
β-strand	264-268	5	4

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	9-13	5	10
β-strand	18-25	8	9
β-strand	32-37	6	10
β-strand	44-49	6	10
β-strand	53-57	5	9
β-strand	60-65	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	84-91	8	10
β-strand	97-99	3	10
β-strand	103-108	6	10
β-strand	117-120	4	11
α-helix	121	1
β-strand	122-123	2	12
β-strand	130-135	6	11
β-strand	151-153	3	11
α-helix	154-156	3
β-strand	157-161	5	11
α-helix	162-164	3
β-strand	166-175	10	11
β-strand	196	1	11

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	31-37	7	14
β-strand	44-51	8	14
β-strand	54-57	4	14
β-strand	65-70	6	13
β-strand	73-78	6	13
α-helix	83-85	3
β-strand	88-94	7	14
α-helix	102-104	3
β-strand	105-106	2	14
β-strand	110-115	6	14
α-helix	118-120	3
β-strand	122	1	15
β-strand	125-130	6	12
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	12
β-strand	152	1	15
β-strand	156-162	7	16
β-strand	165-167	3	16
β-strand	171-173	3	12
β-strand	178-179	2	12
β-strand	189-198	10	12
α-helix	199-202	4
β-strand	208-215	8	16
β-strand	218	1	17
α-helix	229-230	2
β-strand	232	1	17
β-strand	234-241	8	16

Chain F: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-11	5	18
β-strand	15-17	3	19
β-strand	22-27	6	18
β-strand	34-39	6	20
α-helix	52-55	4
β-strand	59-62	4	18
α-helix	67-69	3
β-strand	71-78	8	20
β-strand	83	1	20
α-helix	84-89	6
β-strand	90-92	3	20
β-strand	93-95	3	19
β-strand	102-105	4	21
β-strand	117-122	6	21
β-strand	125	1	5
β-strand	127	1	22
β-strand	129-134	6	23
β-strand	143-145	3	23
α-helix	146-148	3
β-strand	153	1	22
β-strand	157-160	4	21
β-strand	170-177	8	23
β-strand	180-184	5	23
α-helix	186-190	5
β-strand	191-192	2	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major histocompatibility complex class I-related gene protein	A	protein	271	Homo sapiens	Q95460 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
T Cell Receptor Alpha Variable 1-2	D	protein	204	Homo sapiens
T cell receptor beta variable 6-1	E	protein	246	Homo sapiens
Leukocyte immunoglobulin-like receptor subfamily B member 2	F	protein	211	Homo sapiens	Q8N423 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9C9D_1 Major histocompatibility complex class I-related gene protein (chains A)
MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHW
ERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDF
LIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRT
EPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQ
AWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Sequence of entity 2 (B), FASTA

>9C9D_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>9C9D_3 T Cell Receptor Alpha Variable 1-2 (chains D)
MGQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGR
FSSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>9C9D_4 T cell receptor beta variable 6-1 (chains E)
MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGE
VPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Sequence of entity 5 (F), FASTA

>9C9D_5 Leukocyte immunoglobulin-like receptor subfamily B member 2 (chains F)
MQTGTIPKPTLWAEPDSVITQGSPVTLSCQGSLEAQEYRLYREKKSASWITRIRPELVKN
GQFHIPSITWEHTGRYGCQYYSRARWSELSDPLVLVMTGAYPKPTLSAQPSPVVTSGGRV
TLQCESQVAFGGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPNRRWSHRCYGYD
LNSPYVWSSPSDLLELLVPGGSGSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
30W	N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide	C9 H7 N5 O3	1

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

Primary citation

Protein complex. MacLachlan, B. To be published.

Other PDB entries of the same protein (UniProt Q95460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PUD 1.8 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-5'OH-Pentyl-5-OP-U
6PUG 1.8 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-2`OH-Ethyl-5-OP-U
6PUL 1.84 Å, Structure of human MAIT A-F7 TCR in complex with human MR1 3'D-5-OP-RU
7ZT7 1.84 Å, Structure of E8 TCR in complex in human MR1 bound to 5FSA
6PUC 1.85 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU
6PUH 1.88 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-Ribityl-less
6W9U 1.89 Å, Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H-Ac-6-FP
4L4V 1.9 Å, Structure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH
5U6Q 1.9 Å, Structure of human MR1-3-F-SA in complex with human MAIT A-F7 TCR
6PUE 1.9 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-4'D-5-OP-RU
6PUF 1.92 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-5'D-5-OP-RU
6PUJ 1.92 Å, Structure of human MAIT A-F7 TCR in complex with human MR1-3`OH-Propyl-5-OP-U

Browse structure collections

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