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GeezerVison is showing www.rcsb.org — RCSB PDB - 2XSI: Human serum albumin complexed with dansyl-L-glutamate and myristic acid

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  • Biological Assembly 1 (CIF - gz) 
  • Biological Assembly 1 (PDB - gz)
 Data API 

 2XSI | pdb_00002xsi

Human serum albumin complexed with dansyl-L-glutamate and myristic acid

  • PDB DOI: https://doi.org/10.2210/pdb2XSI/pdb
  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Komagataella pastoris
  • Mutation(s): No 

  • Deposited: 2010-10-29 Released: 2010-11-10 
  • Deposition Author(s): Ghuman, J., Curry, S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.251 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2XSI

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

  • Download Mendeley

Structural Basis of Binding of Fluorescent, Site-Specific Dansylated Amino Acids to Human Serum Albumin.

Ryan, A.J., Ghuman, J., Zunszain, P.A., Chung, C.W., Curry, S.

(2011) J Struct Biol 174: 84

  • PubMed: 20940056 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1016/j.jsb.2010.10.004
  • Primary Citation Related Structures: 
    2XSI, 2XVQ, 2XVU, 2XVV, 2XVW, 2XW0, 2XW1

  • PubMed Abstract: 

    Human serum albumin (HSA) has two primary binding sites for drug molecules. These sites selectively bind different dansylated amino acid compounds, which-due to their intrinsic fluorescence-have long been used as specific markers for the drug pockets on HSA. We present here the co-crystal structures of HSA in complex with six dansylated amino acids that are specific for either drug site 1 (dansyl-l-asparagine, dansyl-l-arginine, dansyl-l-glutamate) or drug site 2 (dansyl-l-norvaline, dansyl-l-phenylalanine, dansyl-l-sarcosine). Our results explain the structural basis of the site-specificity of different dansylated amino acids. They also show that fatty acid binding has only a modest effect on binding of dansylated amino acids to drug site 1 and identify the location of secondary binding sites.


  • Organizational Affiliation: 
    • Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, United Kingdom.
Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (9NE)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (9NE)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

  • Total Structure Weight: 68.67 kDa 
  • Atom Count: 4,662 
  • Modeled Residue Count: 582 
  • Deposited Residue Count: 585 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SERUM ALBUMIN
A
585Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
GTEx:  ENSG00000163631 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9NE

Query on 9NE



Download:Ideal Coordinates CCD File
  • SDF format, chain I [auth A]
  • SDF format, chain H [auth A]
  • MOL2 format, chain I [auth A]
  • MOL2 format, chain H [auth A]
  • mmCIF format, chain I [auth A]
  • mmCIF format, chain H [auth A]
H [auth A],
I [auth A]
DANSYL-L-GLUTAMATE
C17 H20 N2 O6 S
OXWKCHDQOLCMPE-ZDUSSCGKSA-N
Interactions
  • Focus chain H [auth A]
  • Focus chain I [auth A]
Interactions & Density
  • Focus chain H [auth A]
  • Focus chain I [auth A]
MYR

Query on MYR



Download:Ideal Coordinates CCD File
  • SDF format, chain B [auth A]
  • SDF format, chain C [auth A]
  • SDF format, chain D [auth A]
  • SDF format, chain G [auth A]
  • SDF format, chain F [auth A]
  • SDF format, chain E [auth A]
  • MOL2 format, chain B [auth A]
  • MOL2 format, chain C [auth A]
  • MOL2 format, chain D [auth A]
  • MOL2 format, chain G [auth A]
  • MOL2 format, chain F [auth A]
  • MOL2 format, chain E [auth A]
  • mmCIF format, chain B [auth A]
  • mmCIF format, chain C [auth A]
  • mmCIF format, chain D [auth A]
  • mmCIF format, chain G [auth A]
  • mmCIF format, chain F [auth A]
  • mmCIF format, chain E [auth A]
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Interactions
  • Focus chain B [auth A]
  • Focus chain C [auth A]
  • Focus chain D [auth A]
  • Focus chain E [auth A]
  • Focus chain F [auth A]
  • Focus chain G [auth A]
Interactions & Density
  • Focus chain B [auth A]
  • Focus chain C [auth A]
  • Focus chain D [auth A]
  • Focus chain E [auth A]
  • Focus chain F [auth A]
  • Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.251 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.26α = 90
b = 38.95β = 105.46
c = 95.39γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2010-11-10 
  • Deposition Author(s): Ghuman, J., Curry, S.

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary
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