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- PDB-9eod: Human serum albumin with adamantene carboxylic acid -

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Basic information

Entry
Database: PDB / ID: 9eod
TitleHuman serum albumin with adamantene carboxylic acid
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / serum albumin
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / platelet alpha granule lumen / fatty acid binding / cellular response to starvation / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
: / MYRISTIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFreitag-Pohl, S. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2020-218 United Kingdom
CitationJournal: To Be Published
Title: Human serum albumin with myristate
Authors: Freitag-Pohl, S. / Pohl, E.
History
DepositionMar 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albumin
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,23914
Polymers139,1662
Non-polymers2,07312
Water4,504250
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7628
Polymers69,5831
Non-polymers1,1807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4766
Polymers69,5831
Non-polymers8935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.860, 38.130, 190.970
Angle α, β, γ (deg.)90.000, 106.152, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 583 / Label seq-ID: 28 - 607

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Albumin


Mass: 69582.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GenBank AAX36126.1 synthetic construct / Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Escherichia coli (E. coli) / References: UniProt: P02768

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Non-polymers , 5 types, 262 molecules

#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-A1H6A / adamantane-1-carboxylic acid


Mass: 180.244 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H16O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.02 % / Description: rods
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM potassium phosphate pH 7.5 31 - 34 % PEG3350 Initial hollow crystals were used as seed stock for seeding experiments.
PH range: 6.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→52.97 Å / Num. obs: 96690 / % possible obs: 98 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Rsym value: 0.11 / Χ2: 1.03 / Net I/σ(I): 5.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
10.4-52.9260.04919.86740.9980.0290.0530.5798.3
1.9-1.936.21.1221.846770.6330.4831.2250.64100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→52.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.35 / SU ML: 0.149 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2683 4876 5.043 %
Rwork0.2168 91814 -
all0.219 --
obs-96690 99.815 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.192 Å2
Baniso -1Baniso -2Baniso -3
1-1.351 Å20 Å21.183 Å2
2---1.094 Å20 Å2
3----0.806 Å2
Refinement stepCycle: LAST / Resolution: 1.9→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 144 250 9186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129133
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168480
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.65412377
X-RAY DIFFRACTIONr_angle_other_deg0.5181.57319532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72251163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.569546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.402101442
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.310376
X-RAY DIFFRACTIONr_chiral_restr0.0790.21424
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021991
X-RAY DIFFRACTIONr_nbd_refined0.2310.22368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.27517
X-RAY DIFFRACTIONr_nbtor_refined0.190.24667
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3890.2310
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.215
X-RAY DIFFRACTIONr_nbd_other0.1910.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.220
X-RAY DIFFRACTIONr_mcbond_it3.9284.0364652
X-RAY DIFFRACTIONr_mcbond_other3.9194.0364651
X-RAY DIFFRACTIONr_mcangle_it5.0037.2325812
X-RAY DIFFRACTIONr_mcangle_other5.0037.2335813
X-RAY DIFFRACTIONr_scbond_it4.964.524481
X-RAY DIFFRACTIONr_scbond_other4.9614.5194478
X-RAY DIFFRACTIONr_scangle_it7.1928.0856564
X-RAY DIFFRACTIONr_scangle_other7.1918.0856565
X-RAY DIFFRACTIONr_lrange_it8.06939.87310587
X-RAY DIFFRACTIONr_lrange_other8.07539.19610553
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.0518146
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079180.05007
12AX-RAY DIFFRACTIONLocal ncs0.079180.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3373770.356607X-RAY DIFFRACTION99.7999
1.949-2.0030.3443580.3256642X-RAY DIFFRACTION99.9857
2.003-2.0610.3413220.36328X-RAY DIFFRACTION99.985
2.061-2.1240.3233390.2826242X-RAY DIFFRACTION100
2.124-2.1930.3173050.2515973X-RAY DIFFRACTION99.9522
2.193-2.270.323050.2365863X-RAY DIFFRACTION99.9352
2.27-2.3560.2832970.2215591X-RAY DIFFRACTION99.966
2.356-2.4520.2763210.2035369X-RAY DIFFRACTION99.9473
2.452-2.5610.2712960.2075207X-RAY DIFFRACTION99.9455
2.561-2.6850.2882530.2274997X-RAY DIFFRACTION99.9619
2.685-2.830.2852420.2284719X-RAY DIFFRACTION99.9396
2.83-3.0010.2772350.2224511X-RAY DIFFRACTION99.9579
3.001-3.2080.2882230.2274253X-RAY DIFFRACTION99.7993
3.208-3.4640.2521980.2073961X-RAY DIFFRACTION99.4263
3.464-3.7930.2521880.2083639X-RAY DIFFRACTION99.7394
3.793-4.2370.2221620.183351X-RAY DIFFRACTION99.9431
4.237-4.8880.2281620.1692901X-RAY DIFFRACTION99.6422
4.888-5.9740.2631150.2132510X-RAY DIFFRACTION99.2814
5.974-8.3950.2591000.211971X-RAY DIFFRACTION98.9962
8.395-52.970.233780.1861179X-RAY DIFFRACTION99.2891

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