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- PDB-9y6c: X-ray structure analysis of human Complement Component 5 TE domai... -

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Basic information

Entry
Database: PDB / ID: 9y6c
TitleX-ray structure analysis of human Complement Component 5 TE domain in complex with the peptide Ra30303
Components
  • Complement C5
  • peptide Ra30303
KeywordsIMMUNE SYSTEM / Complement / C5 / macrocyclic peptide / Myasthenia Gravis
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Regulation of Complement cascade / Peptide ligand-binding receptors / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. ...: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
: / 1,3-dimethylbenzene / Complement C5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYe, P. / Hammer, R.P. / Wang, Z. / Dhamnaskar, K. / Hoarty, M. / Ma, Z. / Tang, G. / DeMarco, S.J. / Ricardo, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Zilucoplan: A Complement C5 Inhibitor for Treatment of Anti-Acetylcholine Receptor (AChR) Antibody-Positive Generalized Myasthenia Gravis (gMG).
Authors: Ye, P. / Hammer, R.P. / Wang, Z. / Dhamnaskar, K. / Hoarty, M. / Ma, Z. / Tang, G.Q. / DeMarco, S.J. / Ricardo, A.
History
DepositionSep 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C5
B: peptide Ra30303
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6584
Polymers38,4602
Non-polymers1982
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-7 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.051, 112.025, 164.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1626-

HOH

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Components

#1: Protein Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4


Mass: 36464.613 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Residues 1123-1134 not included in the model. Occupancy set to 0.00 for residues with side chains not observed in election density: 995, 1005, 1036-1037, 1039, 1042-1043, 1047, 1054, 1122, 1200, 1280, 1305.
Source: (synth.) Homo sapiens (human) / References: UniProt: P01031
#2: Protein/peptide peptide Ra30303


Type: Peptide-like / Class: Inhibitor / Mass: 1995.283 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Occupancy set to 0.00 in the model for residue 3 since side chain electron density not visualized.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002585
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-8VH / 1,3-dimethylbenzene


Type: Peptide-like / Class: Inhibitor / Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002585
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: Proteros

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→82.48 Å / Num. obs: 27129 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.014 / Net I/σ(I): 7.66
Reflection shellResolution: 2→2.25 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.75 / Num. unique obs: 8040 / % possible all: 95.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.6.0117refinement
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→82.48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.908 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25289 1870 6.9 %RANDOM
Rwork0.20646 ---
obs0.20966 25258 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--4.59 Å20 Å2
3----4 Å2
Refinement stepCycle: LAST / Resolution: 2→82.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 6 168 2800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022655
X-RAY DIFFRACTIONr_bond_other_d0.0020.021773
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9733610
X-RAY DIFFRACTIONr_angle_other_deg1.0283.0014307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9435324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20724.554112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94815434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0731510
X-RAY DIFFRACTIONr_chiral_restr0.060.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 136 -
Rwork0.38 1737 -
obs--96.3 %

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