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9vx3

Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp

Method: X-RAY DIFFRACTION D_max: 102.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vx3
deposition_date	2025-07-18
title	Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp
keywords	HisMab-1, Fv-clasp, His-tag, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	31.65 Å
rg_electron	30.85 Å
i0	92913600.00
molecular_weight	74296.0 kDa
excluded_volume	92266 Å³
envelope_volume	120940 Å³
shell_volume	34162 Å³
envelope_diameter	101.6 Å
shell_rg	36.65 Å
envelope_rg	30.11 Å
shape_rg	30.90 Å
total_rg	31.24 Å
total_atoms	5218
n_residues	637
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	102.1 Å
rg_real	31.69 Å
rg_real_error	1.12 Å
i0_real	9.2910e+07
i0_real_error	1.5640e+06
rg_reciprocal	31.68 Å
i0_reciprocal	92910000.0000
total_estimate	0.9007
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.301
kurtosis	-0.617
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	11840000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.939

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit
formula_weight	19744.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	5230

GREVQLQQFGAELVKPGASVKISCKASGYTFTDYNMDWVKQSHGKSLEWIGDINPNYDSTVYNQKFKGKATLTVDKSSSTAYMELRSLTSEDTAIYYCARDGAYAMDHWGQGTSVTVCSGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAKGTLLG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	HisMab-1VL,Serine/threonine-protein kinase 4 18kDa subunit
formula_weight	18680.1 kDa
mutation	S37C
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

GRDIVMTQSPSSLSVSAGEKVTMSCKSSQSLLNSGHQKNYLAWYQQKPGQPPKLLISGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHRYPLTFGAGTKLELKRGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Polyhistidine peptide
formula_weight	846.9 kDa
src_method	syn
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

HHHHHH

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (1)

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length_a	54.139 Å
length_b	69.512 Å
length_c	93.396 Å
angle_alpha	90.00 °
angle_beta	93.78 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.390 Å
resolution_low	39.570 Å
r_factor	0.1976
r_work	0.1956
r_free	0.2370

fit	/app/data/saxs_computation/vx/9vx3/9vx3.fit
pddf	/app/data/pr_computation/vx/9vx3/9vx3.pr.out
profile	/app/data/saxs_computation/vx/9vx3/9vx3.dat

Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)