9WJ6: Peptide from GTPase KRas, N-terminally processed

An integrated in silico-in vitro workflow for discovering high-affinity, selective antibodies to the KRAS(G12D)-MHC I complex. Determined by X-ray diffraction at 4.54 Å resolution. Released 24 Jun 2026.

Method: X-ray diffraction
Resolution: 4.54 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,930
Mol. weight: 196.79 kDa
Released: 24 Jun 2026

Explore 9WJ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9WJ6 contains 62 α-helices and 150 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.

Chains A and K: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-12	4	2
β-strand	18-23	6	1
α-helix	27-29	3
β-strand	33-37	5	2
β-strand	44-47	4	2
β-strand	48	1	3
β-strand	52	1	3
β-strand	61-66	6	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	83-91	9	2
β-strand	96-99	4	2
β-strand	103-107	5	2
β-strand	112	1	4
α-helix	113-114	2
β-strand	115-119	5	5
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	5
β-strand	141	1	4
β-strand	146-151	6	6
β-strand	154-155	2	6
α-helix	156	1
β-strand	160-164	5	5
α-helix	165-168	4
β-strand	174-183	10	5
α-helix	184-187	4
β-strand	192-198	7	6
β-strand	206-211	6	6

Chains B and L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	46-51	6	13
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	109-112	4	13
β-strand	116-118	3	13
β-strand	119-120	2	12
α-helix	124-125	2
β-strand	126	1	14
β-strand	129-133	5	15
α-helix	134-136	3
α-helix	140	1
β-strand	144-154	11	15
β-strand	155	1	14
β-strand	160-163	4	16
α-helix	164-166	3
β-strand	172-174	3	15
α-helix	175-177	3
β-strand	178-179	2	15
β-strand	185-194	10	15
α-helix	195-199	5
β-strand	203-209	7	16
α-helix	210-212	3
β-strand	214-220	7	16

Chains E and M: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	7
α-helix	20	1
β-strand	21-28	8	7
β-strand	31-37	7	7
β-strand	46-47	2	7
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	7
β-strand	111-118	8	7
β-strand	121-126	6	7
β-strand	133-135	3	7
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	8
α-helix	184-185	2
β-strand	186-193	8	9
β-strand	198-208	11	9
β-strand	209	1	8
β-strand	214-219	6	10
β-strand	222-223	2	10
β-strand	228-230	3	9
α-helix	231-233	3
β-strand	234-235	2	9
β-strand	241-250	10	9
α-helix	254-256	3
β-strand	257-262	6	10
β-strand	270-272	3	10

Chains F and N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	17
β-strand	3	1	18
α-helix	4-5	2
β-strand	6-11	6	19
β-strand	21-30	10	19
β-strand	31	1	18
β-strand	36-41	6	20
β-strand	44-45	2	20
α-helix	46	1
β-strand	50-51	2	19
β-strand	55-56	2	19
β-strand	62-70	9	19
β-strand	78-83	6	20
β-strand	91-94	4	20

Chains I and P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptide from GTPase KRas, N-terminally processed	I, P	protein	10	Homo sapiens	P01116 (AlphaFold model)
C8K10D5-1 Fab Light chain	A, K	protein	234	Homo sapiens
HLA class I antigen	E, M	protein	280	Homo sapiens	C1K0Y1 (AlphaFold model)
C8K10D5-1 Fab heavy chain	B, L	protein	255	Homo sapiens
Beta-2-microglobulin	F, N	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (I, P), FASTA

>9WJ6_1 Peptide from GTPase KRas, N-terminally processed (chains I, P)
GADGVGKSAL

Sequence of entity 2 (A, K), FASTA

>9WJ6_2 C8K10D5-1 Fab Light chain (chains A, K)
MGWSCIILFLVATATGVHSSYVLTQPPSVSVAPGQTARITCGGNNIKYRDVHWYQQKPGQ
APVLVVYQDTLRPQGIPERFSGSNSGNMATLTISRVEAGDEADYYCQVWDWDTDHWVFGG
GTDLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, M), FASTA

>9WJ6_3 HLA class I antigen (chains E, M)
MSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDG
KDYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWHHHHHH

Sequence of entity 4 (B, L), FASTA

>9WJ6_4 C8K10D5-1 Fab heavy chain (chains B, L)
MGWSCIILFLVATATGVHSEVQLVESGGGLVQPGRSLRLSCAASGFTFDQYAMHWVRQAP
GKGLEWVSGISAYSLSIGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARGRS
EGVYMDGMDIWGSGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE
PKSCDKTHHHHHHHH

Sequence of entity 5 (F, N), FASTA

>9WJ6_5 Beta-2-microglobulin (chains F, N)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Primary citation

Discovery of TCR-like antibodies to the KRAS G12D neoantigen via in silico-in vitro workflow. Ahn, S., Oh, T.S., Suh, S. et al. Mol Ther (2026) 34:5157-5174. DOI 10.1016/j.ymthe.2026.05.032 · PubMed

Other PDB entries of the same protein (UniProt P01116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IAY 0.95 Å, Structure of 10 in complex with GDP-KRAS
9IAW 1.0 Å, Structure of 5 in complex with GDP-KRAS
12XE 1.01 Å, Crystal structure of KRAS(Q61K) bound to GppNHp and ligand
8ONV 1.01 Å, KRAS-G13D in complex with BI-2493
6P0Z 1.01 Å, Crystal structure of N-acetylated KRAS (2-169) bound to GDP and Mg
9IB5 1.01 Å, Structure of 18 (BI-2493) in complex with GDP-KRAS
8AZZ 1.02 Å, KRAS-G12V in complex with BI-2865
8AZX 1.04 Å, KRAS-G12C in complex with BI-2865
8B00 1.04 Å, KRAS-G13D in complex with BI-2865
8TVK 1.04 Å, KRAS 1-169 G12C Mutant at 100k
4QL3 1.04 Å, Crystal Structure of a GDP-bound G12R Oncogenic Mutant of Human GTPase KRas
8AZV 1.05 Å, KRAS in complex with BI-2865

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