3TDL

Structure of human serum albumin in complex with DAUDA

• PDB DOI: https://doi.org/10.2210/pdb3TDL/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2011-08-11 Released: 2012-06-27 
• Deposition Author(s): Wang, Y., Luo, Z., Shi, X., Wang, H., Nie, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

A fluorescent fatty acid probe, DAUDA, selectively displaces two myristates bound in human serum albumin

Wang, Y., Luo, Z., Shi, X., Wang, H., Nie, L., Huang, M.

(2011) Protein Sci 20: 2095-2101

• PubMed: 21997768 
• DOI: https://doi.org/10.1002/pro.749
• Primary Citation of Related Structures:  
  3TDL


• PubMed Abstract: 
  

  11-(Dansylamino) undecanoic acid (DAUDA) is a dansyl-type fluorophore and has widely used as a probe to determine the binding site for human serum albumin (HSA). Here, we reported that structure of HSA-Myristate-DAUDA ternary complex and identified clearly the presence of two DAUDA molecules at fatty acid (FA) binding site 6 and 7 of HSA, thus showing these two sites are weak FA binding sites. This result also show that DAUDA is an appropriate probe for FA site 6 and 7 on HSA as previous studied, but not a good probe of FA binding site 1 that is likely bilirubin binding site on HSA.

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Organizational Affiliation: 

State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.35 kDa 
• Atom Count: 4,720 
• Modelled Residue Count: 578 
• Deposited Residue Count: 585 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A	585	Homo sapiens	Mutation(s): 0  Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768  Go to UniProtKB:  P02768
PHAROS:  P02768 GTEx:  ENSG00000163631

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
11D	F [auth A], G [auth A]	11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid C23 H34 N2 O4 S CEPGVMDMVJGHFQ-UHFFFAOYSA-N
MYR	B [auth A], C [auth A], D [auth A], E [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.261 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.657	α = 90
b = 37.137	β = 104.38
c = 90.195	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Wang, Y., Luo, Z., Shi, X., Wang, H., Nie, L.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary