SAXSdb — 9xy4

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1. Structure Basics

entry_id	9xy4
deposition_date	2025-08-25
title	Zymogen ADAM17- iRhom1 Cytoplasmic Deletion (370) Complex Bound by the MEDI3622 Fab
keywords	Complex, Membrane Protein, Enzyme, ADAM, Rhomboid, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

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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	43.69 Å
rg_electron	44.81 Å
i0	322181000.00
molecular_weight	145650.0 kDa
excluded_volume	181420 Å³
envelope_volume	253820 Å³
shell_volume	49894 Å³
envelope_diameter	159.0 Å
shell_rg	46.12 Å
envelope_rg	44.39 Å
shape_rg	44.84 Å
total_rg	44.79 Å
total_atoms	10223
n_residues	1279
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	148.5 Å
rg_real	43.95 Å
rg_real_error	1.35 Å
i0_real	3.2220e+08
i0_real_error	5.6110e+06
rg_reciprocal	43.69 Å
i0_reciprocal	322100000.0000
total_estimate	0.8433
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.1 Å
skewness	0.433
kurtosis	-0.389
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	29010000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.548

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Inactive rhomboid protein 1
formula_weight	48959.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10223

MDDHRPFFTYWLTFVHSLVTILAVCIYGIAPVGFSQHETVDSVLRNRGVYENVKYVQQENFWIGPSSEALIHLGAKFSPCMRQDPQVHSFIRSAREREKHSACCVRNDRSGCVQTSEEECSSTLAVWVKWPIHPSAPELAGHKRQFGSVCHQDPRVCDEPSSEDPHEWPEDITKWPICTKNSAGNHTNHPHMDCVITGRPCCIGTKGRCEITSREYCDFMRGYFHEEATLCSQVHCMDDVCGLLPFLNPEVPDQFYRLWLSLFLHAGILHCLVSICFQMTVLRDLEKLAGWHRIAIIYLLSGVTGNLASAIFLPYRAEVGPAGSQFGILACLFVELFQSWQILARPWRAFFKLLAVVLFLFTFGLLPWIDNFAHISGFISGLFLSFAFLPYISFGKFDLYRKRCQIIIFQVVFLGLLAGLVVLFYVYPV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	MEDI3622 Fab Heavy Chain
formula_weight	23324.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

DIQMTQSPSSLSASVGDRVTITCRSSQSIPSYLNWYQQKPGKAPKLLIYAASRLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	MEDI3622 Fab Light Chain
formula_weight	22900.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYPMNWVRQAPGKGLEWVSYISPFGGMTDYATSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDAMRGAEVDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Disintegrin and metalloproteinase domain-containing protein 17
formula_weight	76130.9 kDa
ec_number	3.4.24.86
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

PHQRLEKLDSLLSDYDILSLSNIQQHSVRKRDLQTSTHVETLLTFSALKRHFKLYLTSSTERFSQNFKVVVVDGKNESEYTVKWQDFFTGHVVGEPDSRVLAHIRDDDVIIRINTDGAEYNIEPLWRFVNDTKDKRMLVYKSEDIKNVSRLQSPKVCGYLKVDNEELLPKGLVDREPPEELVHRVKRRADPDPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTSWDNAGFKGYGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCLAHLFTYQDFDMGTLGLAYVGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTILTKEADLVTTHALGHNFGAEHDPDGLAECAPNEDQGGKYVMYPIAVSGDHENNKMFSNCSKQSIYKTIESKAQECFQERSNKVCGNSRVDEGEECDPGIMYLNNDTCCNSDCTLKEGVQCSDRNSPCCKNCQFETAQKKCQEAINATCKGVSYCTGNSSECPPPGNAEDDTVCLDLGKCKDGKCIPFCEREQQLESCACNETDNSCKVCCRDLSGRCVPYVDAEQKNLFLRKGKPCTVGFCDMNGKCEKRVQDVIERFWDFIDQLSINTFGKFLADNIVGSVLVFSLIFWIPFSILVHCVDKKL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	6

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.12 Å
resolution_method	—
num_particles	34630

fit	/app/data/saxs_computation/xy/9xy4/9xy4.fit
pddf	/app/data/pr_computation/xy/9xy4/9xy4.pr.out
profile	/app/data/saxs_computation/xy/9xy4/9xy4.dat

Zymogen ADAM17- iRhom1 Cytoplasmic Deletion (370) Complex Bound by the MEDI3622 Fab

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)