9VX3: Peptide-bound form of HisMab-1 Fv-clasp

Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp. Determined by X-ray diffraction at 2.39 Å resolution. Released 17 Dec 2025.

Method: X-ray diffraction
Resolution: 2.39 Å
Organisms: Mus musculus, Homo sapiens, synthetic construct
Chains: 6
Atoms: 5,230
Mol. weight: 78.54 kDa
Released: 17 Dec 2025

Explore 9VX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VX3 contains 21 α-helices and 52 β-strands across 4 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: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	3
β-strand	45-52	8	3
β-strand	56-59	4	3
α-helix	61-63	3
β-strand	64	1	1
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
β-strand	100-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	119-122	4
α-helix	125-163	39

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10	1	5
β-strand	19-25	7	4
β-strand	30-30A	2	6
β-strand	30F-31	2	6
β-strand	33-38	6	5
β-strand	45-49	5	5
β-strand	53-54	2	5
α-helix	55	1
β-strand	62-67	6	4
β-strand	70-75	6	4
α-helix	80-82	3
β-strand	85-90	6	5
α-helix	96	1
β-strand	98	1	5
β-strand	102-103	2	5
α-helix	120-156	37

Chain D: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	17-25	9	7
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	45-52	8	9
β-strand	56-59	4	9
α-helix	61-63	3
β-strand	64	1	7
β-strand	67-72	6	7
β-strand	77-82A	7	7
α-helix	84-86	3
β-strand	88-95	8	9
β-strand	100-103	4	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	117-120	4
α-helix	125-163	39

Chain E: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	9
β-strand	19-25	7	10
β-strand	30-30A	2	11
β-strand	30F-31	2	11
β-strand	33-38	6	9
α-helix	43-44	2
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
α-helix	120-148	29
α-helix	150-156	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit	A, D	protein	175	Mus musculus, Homo sapiens	Q13043 (AlphaFold model)
HisMab-1VL,Serine/threonine-protein kinase 4 18kDa subunit	B, E	protein	167	Mus musculus, Homo sapiens	Q13043 (AlphaFold model)
Polyhistidine peptide	C, F	protein	6	synthetic construct

Sequence of entity 1 (A, D), FASTA

>9VX3_1 HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit (chains A, D)
GREVQLQQFGAELVKPGASVKISCKASGYTFTDYNMDWVKQSHGKSLEWIGDINPNYDST
VYNQKFKGKATLTVDKSSSTAYMELRSLTSEDTAIYYCARDGAYAMDHWGQGTSVTVCSG
SDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAKGTLLG

Sequence of entity 2 (B, E), FASTA

>9VX3_2 HisMab-1VL,Serine/threonine-protein kinase 4 18kDa subunit (chains B, E)
GRDIVMTQSPSSLSVSAGEKVTMSCKSSQSLLNSGHQKNYLAWYQQKPGQPPKLLISGAS
TRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHRYPLTFGAGTKLELKRGSDY
EFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAK

Sequence of entity 3 (C, F), FASTA

>9VX3_3 Polyhistidine peptide (chains C, F)
HHHHHH

Primary citation

Functional and Structural Characterization of a Novel Anti-His-tag Antibody, HisMab-1. Hitomi, N., Hoshi, S., Kaneko, M.K. et al. J Mol Biol (2025) 438:169574-169574. DOI 10.1016/j.jmb.2025.169574 · PubMed

Other PDB entries of the same protein (UniProt Q13043 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAV 1.9 Å, Crystal structure of MST1 with a MAP4K1 SMOL inhibitor
4NR2 2.0 Å, Crystal structure of STK4 (MST1) SARAH domain
8A5J 2.12 Å, Crystal structure of Human STE20-like kinase 1, MST1 in complex with compound XMU-MP-1
8PAW 2.14 Å, Crystal structure of MST1 with a MAP4K1 SMOL inhibitor
3COM 2.2 Å, Crystal structure of Mst1 kinase
4OH8 2.28 Å, Crystal Structure of the human MST1-RASSF5 SARAH heterodimer
5TWG 2.3 Å, human MOB1A bound to human MST1 phosphorylated T353 peptide
5TWH 2.5 Å, human MOB1A bound to MST1 phosphorylated T367 peptide
7CEA 2.55 Å, Crystal structure of HUTS-4 Fv-clasp fragment
6YAT 2.58 Å, Crystal structure of STK4 (MST1) in complex with compound 6
9IIC 2.78 Å, Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain
7CEB 2.89 Å, Crystal structure of alpha6beta1 integrin headpiece

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