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- PDB-3jqz: Crystal Structure of Human serum albumin complexed with Lidocaine -

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Basic information

Entry
Database: PDB / ID: 3jqz
TitleCrystal Structure of Human serum albumin complexed with Lidocaine
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / ALBUMIN / CARRIER PROTEIN / DRUG-BINDING / Lidocaine / Alternative splicing / Cleavage on pair of basic residues / Copper / Disease mutation / Disulfide bond / Glycation / Glycoprotein / Lipid-binding / Metal-binding / Phosphoprotein / Polymorphism / Secreted
Function / homology
Function and homology information


exogenous protein binding / enterobactin binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / enterobactin binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / 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 / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / 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 / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / 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 ...Serum Albumin; Chain A, Domain 1 - #10 / 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 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-(diethylamino)-N-(2,6-dimethylphenyl)ethanamide / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHein, K.L. / Kragh-Hansen, U. / Morth, J.P. / Nissen, P.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystallographic analysis reveals a unique lidocaine binding site on human serum albumin.
Authors: Hein, K.L. / Kragh-Hansen, U. / Morth, J.P. / Jeppesen, M.D. / Otzen, D. / Moller, J.V. / Nissen, P.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3773
Polymers133,1422
Non-polymers2341
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-14 kcal/mol
Surface area53680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.476, 168.476, 97.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLNGLNchain A, 1-196AA1 - 1961 - 196
21ASPASPGLNGLNchain B, 1-196BB1 - 1961 - 196
12ARGARGILEILEchain A, 197-388AA197 - 388197 - 388
22ARGARGILEILEchain B, 197-388BB197 - 388197 - 388
13LYSLYSALAALAchain A, 389-582AA389 - 582389 - 582
23LYSLYSALAALAchain B, 389-582BB389 - 582389 - 582

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Pichia pastoris (fungus) / References: UniProt: P02768
#2: Chemical ChemComp-LQZ / 2-(diethylamino)-N-(2,6-dimethylphenyl)ethanamide


Mass: 234.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-21% polyethylene glycol 6000, 9-10% ethylene glycol, 50/100mM ammonium acetate, 2% 2-methyl-2,4-pentanediol, 50mM Tris-HCl, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.3→119.523 Å / Num. all: 20529 / Num. obs: 20507 / % possible obs: 99.9 % / Observed criterion σ(I): 1.1 / Redundancy: 6.3 % / Biso Wilson estimate: 110.675 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 13.04
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.16 / Num. unique all: 3249 / % possible all: 100

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Processing

Software
NameClassification
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BXE

2bxe


Resolution: 3.3→44.928 Å / SU ML: -0 / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 1054 5.14 %Random
Rwork0.2203 ---
obs0.2227 20503 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 98.279 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso mean: 142.359 Å2
Refinement stepCycle: LAST / Resolution: 3.3→44.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9262 0 17 0 9279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039493
X-RAY DIFFRACTIONf_angle_d0.71512762
X-RAY DIFFRACTIONf_dihedral_angle_d22.3075880
X-RAY DIFFRACTIONf_chiral_restr0.051414
X-RAY DIFFRACTIONf_plane_restr0.0031665
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1577X-RAY DIFFRACTIONPOSITIONAL
12B1577X-RAY DIFFRACTIONPOSITIONAL1.228
21A1526X-RAY DIFFRACTIONPOSITIONAL
22B1526X-RAY DIFFRACTIONPOSITIONAL0.943
31A1529X-RAY DIFFRACTIONPOSITIONAL
32B1529X-RAY DIFFRACTIONPOSITIONAL0.813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.45030.361410.32912368X-RAY DIFFRACTION100
3.4503-3.63220.35211290.30472408X-RAY DIFFRACTION100
3.6322-3.85960.34641250.28592436X-RAY DIFFRACTION100
3.8596-4.15740.33321500.23722419X-RAY DIFFRACTION100
4.1574-4.57550.26051280.21412429X-RAY DIFFRACTION100
4.5755-5.23670.22851240.2042446X-RAY DIFFRACTION100
5.2367-6.59430.3191360.23632442X-RAY DIFFRACTION100
6.5943-44.93210.1831210.15622501X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.5228-0.0628-0.59483.4313-0.72732.704-0.00270.30870.27310.28560.56150.3667-0.2059-0.129-0.57260.91160.10510.1270.89010.15951.237120.2206-15.4854-53.7831
22.45731.7417-1.56882.20810.70665.0081-0.09460.05160.0845-0.14380.36360.13510.11640.0754-0.26231.1055-0.0483-0.22551.12490.23291.5283
31.78680.1451-0.84454.0443-0.75551.29850.1482-0.85090.04490.7777-0.0213-0.1602-0.23610.4079-0.13621.29560.09630.04111.5511-0.32341.0268
43.6233-0.4001-0.76523.8606-0.54122.36090.3775-0.0249-0.1324-0.46320.1168-0.31210.1775-0.2993-0.50921.4528-0.1297-0.33561.28080.26211.1649
53.8279-0.4596-2.1873.40491.41115.4256-0.02690.5262-0.2558-0.217-0.011-0.15760.0534-0.17560.03180.87830.0478-0.05410.98830.03020.8383
62.3441-0.06840.50972.7749-1.47936.96850.3679-0.00750.3061-0.11190.1020.5195-0.04910.5287-0.48250.978-0.14370.01861.08580.17190.8697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A, 1-196A1 - 196
2X-RAY DIFFRACTION2chain B, 1-196B1 - 196
3X-RAY DIFFRACTION3chain A, 197-388A197 - 388
4X-RAY DIFFRACTION4chain B, 197-388B197 - 388
5X-RAY DIFFRACTION5chain A, 389-582A389 - 582
6X-RAY DIFFRACTION6chain B, 389-582B389 - 582

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