[English] 日本語
Yorodumi
- PDB-6fty: COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fty
TitleCOMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 5
ComponentsComplement factor D
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / protein maturation / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / protein maturation / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-E7H / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsOstermann, N.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D.
Authors: Vulpetti, A. / Ostermann, N. / Randl, S. / Yoon, T. / Mac Sweeney, A. / Cumin, F. / Lorthiois, E. / Rudisser, S. / Erbel, P. / Maibaum, J.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1843
Polymers24,7391
Non-polymers4452
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.326, 49.861, 39.427
Angle α, β, γ (deg.)90.00, 105.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Complement factor D / Adipsin / C3 convertase activator / Properdin factor D


Mass: 24739.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-E7H / 4-[[(5~{S},7~{R})-3-azanyl-1-adamantyl]carbonylamino]-1~{H}-indole-2-carboxamide


Mass: 352.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N4O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsP2SEQ ANNOTATION (DBREF, SEQADV, MODRES, REMARK 465, COMPND, SOURCE RECORDS) WAS ADDED SEMI- ...P2SEQ ANNOTATION (DBREF, SEQADV, MODRES, REMARK 465, COMPND, SOURCE RECORDS) WAS ADDED SEMI-AUTOMATICALLY TO THIS ENTRY. CONSTRUCT BOUNDARIES IN DBREF MAY BE INACCURATE IF THE ORIGINAL DEPOSITION DID NOT SPECIFY A PROTRACK CRYSTALLIZATION SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 100 mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→53.22 Å / Num. obs: 23224 / % possible obs: 96.2 % / Redundancy: 3.15 % / Biso Wilson estimate: 11.82 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.73
Reflection shellResolution: 1.67→1.74 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 5.81 / % possible all: 88.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.11.7refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FBE

5fbe


Resolution: 1.67→53.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.106 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1162 5 %RANDOM
Rwork0.171 ---
obs0.173 23224 96.4 %-
Displacement parametersBiso mean: 14.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.317 Å20 Å20.0076 Å2
2---2.9582 Å20 Å2
3---1.6413 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.67→53.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 32 171 1915
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011828HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092505HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d620SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1828HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion15.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2233SEMIHARMONIC4
LS refinement shellResolution: 1.67→1.74 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2494 129 5.02 %
Rwork0.2155 2442 -
all0.2172 2571 -
obs--89.22 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more