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9qn5

Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space group.

Method: X-RAY DIFFRACTION D_max: 128.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qn5
deposition_date	2025-03-24
last_revision	2026-04-08
title	Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space group.
keywords	SUMO, SUMOylation, heterodimer, Aos1, Uba2, SIGNALING PROTEIN; SIGNALING PROTEIN
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	39.95 Å
rg_electron	39.44 Å
i0	506226000.00
molecular_weight	184690.0 kDa
excluded_volume	231570 Å³
envelope_volume	308840 Å³
shell_volume	64072 Å³
envelope_diameter	134.6 Å
shell_rg	46.64 Å
envelope_rg	38.43 Å
shape_rg	39.46 Å
total_rg	39.78 Å
total_atoms	12969
n_residues	1642
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	128.4 Å
rg_real	39.84 Å
rg_real_error	0.83 Å
i0_real	5.0620e+08
i0_real_error	8.2900e+06
rg_reciprocal	39.95 Å
i0_reciprocal	506300000.0000
total_estimate	0.8949
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.1 Å
skewness	0.205
kurtosis	-0.464
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	78600000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.870

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	SUMO-activating enzyme subunit 1
formula_weight	40960.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13159

MGSSHHHHHHSSGLVPRGSHMASMVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGVKGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPESFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTKVAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDYFLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMAPVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	SUMO-activating enzyme subunit 2
formula_weight	71314.5 kDa
ec_number	2.3.2.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTIDVSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNVEFFRQFILVMNALDNRAARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPTEAEARARASNEDGDIKRISTKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQNEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNKQPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDLGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQDDVLIVDSDEEDSSNNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	176

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6. Citations (1)

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length_a	91.470 Å
length_b	115.562 Å
length_c	98.571 Å
angle_alpha	90.00 °
angle_beta	104.70 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.970 Å
resolution_low	73.540 Å
r_factor	0.2011
r_work	0.1989
r_free	0.2439

fit	/app/data/saxs_computation/qn/9qn5/9qn5.fit
pddf	/app/data/pr_computation/qn/9qn5/9qn5.pr.out
profile	/app/data/saxs_computation/qn/9qn5/9qn5.dat

Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space group.

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)