9PKF: Mur35 Fab with HBV c18I pMHC

Mur35 Fab with HBV c18I pMHC. Determined by X-ray diffraction at 2.6 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus, Hepatitis B virus
Chains: 5
Atoms: 6,045
Mol. weight: 96.53 kDa
Released: 1 Oct 2025

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

Secondary structure: helices and β-sheets

9PKF contains 23 α-helices and 74 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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	199-208	10	3
β-strand	209	1	2
β-strand	214-216	3	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-247	7	3
β-strand	259-262	4	4
β-strand	270-272	3	4

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	18
α-helix	14-15	2
β-strand	21-30	10	18
β-strand	36-41	6	19
β-strand	44-45	2	19
β-strand	50-51	2	18
β-strand	55-56	2	18
β-strand	62-70	9	18
β-strand	78-83	6	19
β-strand	91-94	4	19

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	10-12	3	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	64	1	5
β-strand	67-72	6	5
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	89-95	7	7
α-helix	96	1
β-strand	100A-103	4	7
β-strand	107-108	2	7
β-strand	109-111	3	6
β-strand	122-124	3	8
β-strand	139-141	3	8
β-strand	145	1	9
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	164-165	2	8
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-177	2	9
β-strand	179-181	3	8
β-strand	196-199	4	10
β-strand	200	1	11
β-strand	205	1	11

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
α-helix	30-32	3
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-90	6	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-106	5	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	116-118	3	15
β-strand	132-139	8	15
β-strand	140	1	14
β-strand	146-147	2	16
β-strand	149	1	17
β-strand	154	1	17
β-strand	159-160	2	15
β-strand	163	1	15
α-helix	164-167	4
β-strand	173-179	7	15
α-helix	183-186	4
β-strand	195-196	2	16
β-strand	205	1	16

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	301	Homo sapiens	Q8WLS4 (AlphaFold model)
Mur35 Heavy Chain	H	protein	237	Mus musculus
Mur35 Light Chain	L	protein	215	Mus musculus
c18I peptide	P	protein	10	Hepatitis B virus	P69707
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9PKF_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGGSGGSAGGGLNDIFEAQKIE
W

Sequence of entity 2 (H), FASTA

>9PKF_2 Mur35 Heavy Chain (chains H)
EVQLQQSGPELVKPGASVKISCKASGYTFTDHFMNWVRQSHGKSLEWIGDINPNNGGTSY
NQKFKGKATLTVDKSSSTAFMEVRSLTSDDSAVYYCARRGYYGSFDYWGQGTTLTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHHHHDYKDDDDK

Sequence of entity 3 (L), FASTA

>9PKF_3 Mur35 Light Chain (chains L)
EIVMTQSPATLSLSPGERATLSCRASQGVSSSYFSWYQQTPGQAPRLLISGASTRATGIP
ARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDYNLPYTFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (P), FASTA

>9PKF_4 c18I peptide (chains P)
FLPSDFFPSI

Sequence of entity 5 (B), FASTA

>9PKF_5 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Primary citation

A highly selective TCR-mimic antibody reveals unexpected mechanisms of HBV peptide-MHC recognition and previously unknown target biology. Khan, S., Lum, J., Stephenson, H. et al. MAbs (2025) 17:2562998-2562998. DOI 10.1080/19420862.2025.2562998 · PubMed

Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X7U 1.59 Å, Complex of HLA-A2, a class I MHC, with a UTP20 peptide
9WK0 1.8 Å, Neoantigen Rac1P29S-HLA-A2
21GJ 1.83 Å, Neoantigen p53Y220D-HLA-A2
21EX 2.02 Å, Wild tipe p53WT-HLA-A2
9XME 2.04 Å, Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide
9J4U 2.17 Å, Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by…
9PIX 2.35 Å, Mur14 Fab with HBV c18V pMHC
9PKC 2.5 Å, Mur35 Fab with HBV c18V pMHC
9PKV 2.72 Å, HU-38 Fab with PRAME pMHC
9LLU 2.87 Å, p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2
3HG1 3.0 Å, Germline-governed recognition of a cancer epitope by an immunodominant human T cell…
9C96 3.0 Å, Cryo-EM structure of TAP binding protein related (TAPBPR) in complex with HLA-A*02:01…

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