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9y6c

X-ray structure analysis of human Complement Component 5 TE domain in complex with the peptide Ra30303

Method: X-RAY DIFFRACTION D_max: 69.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y6c
deposition_date	2025-09-08
title	X-ray structure analysis of human Complement Component 5 TE domain in complex with the peptide Ra30303
keywords	Complement, C5, macrocyclic peptide, Myasthenia Gravis, 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	20.70 Å
rg_electron	19.77 Å
i0	42725000.00
molecular_weight	34596.0 kDa
excluded_volume	33860 Å³
envelope_volume	54358 Å³
shell_volume	22443 Å³
envelope_diameter	67.2 Å
shell_rg	26.75 Å
envelope_rg	20.09 Å
shape_rg	19.73 Å
total_rg	20.53 Å
total_atoms	2632
n_residues	323
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	69.3 Å
rg_real	21.08 Å
rg_real_error	0.17 Å
i0_real	4.2200e+07
i0_real_error	4.6150e+05
rg_reciprocal	20.60 Å
i0_reciprocal	42730000.0000
total_estimate	0.6849
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	66.3 Å
skewness	0.325
kurtosis	-0.134
angular_range	— – 0.3850 Å⁻¹
current_alpha	6.2490
highest_alpha	14260000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 0.925; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.628

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Complement C5
formula_weight	36464.6 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2800

LLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSDPLIEKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQNSICNSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFDICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDKTHPQFRSIVSALKREALVKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEEQRYGGGFYSTQDTINAIEGLTEYSLLVK

Entity 2 polymer

description	peptide Ra30303
formula_weight	1995.3 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

XCVERFCDVYWEYPAVX

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,3-dimethylbenzene
formula_weight	106.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	168

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6. Citations (1)

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length_a	45.051 Å
length_b	112.025 Å
length_c	164.968 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.000 Å
resolution_low	82.480 Å
r_factor	0.2097
r_work	0.2065
r_free	0.2529

fit	/app/data/saxs_computation/y6/9y6c/9y6c.fit
pddf	/app/data/pr_computation/y6/9y6c/9y6c.pr.out
profile	/app/data/saxs_computation/y6/9y6c/9y6c.dat

X-ray structure analysis of human Complement Component 5 TE domain in complex with the peptide Ra30303

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)