4JK4

Crystal Structure of Bovine Serum Albumin in complex with 3,5-diiodosalicylic acid

PDB DOI: https://doi.org/10.2210/pdb4JK4/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bos taurus
Mutation(s): Yes

Deposited: 2013-03-09 Released: 2013-07-24
Deposition Author(s): Zielinski, K., Bujacz, A., Sekula, B., Bujacz, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.246
R-Value Work: 0.188
R-Value Observed: 0.191

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystallographic studies of the complexes of bovine and equine serum albumin with 3,5-diiodosalicylic acid.

Sekula, B., Zielinski, K., Bujacz, A.

(2013) Int J Biol Macromol 60C: 316-324

PubMed: 23769932 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2013.06.004
Primary Citation of Related Structures:
4J2V, 4JK4

PubMed Abstract:
Due to their extraordinary binding properties, serum albumins are the main transporters of many small molecules in the circulatory system. Although all mammalian serum albumins exhibit quite high sequence similarity, their binding abilities are not the same. Until now, only human serum albumin (HSA) was subjected to extensive structural studies in complexes with various ligands. Here we present two crystal structures of the complexes of equine and bovine serum albumins with 3,5-diiodosalicylic acid (DIS), at resolutions 2.12 Å and 2.65 Å, respectively, and analyze interactions of the DIS ligand with both macromolecules. We highlight the differences in distribution of DIS binding sites between the bovine and equine serum albumins and compare results with the HSA binding ability of DIS and other structurally similar ligands.

Organizational Affiliation

Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland.

Macromolecule Content

Total Structure Weight: 137.75 kDa
Atom Count: 9,643
Modelled Residue Count: 1,164
Deposited Residue Count: 1,166
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A, B	583	Bos taurus	Mutation(s): 1
UniProt
Find proteins for P02769 (Bos taurus) Explore P02769 Go to UniProtKB: P02769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DIU Query on DIU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] O [auth B] C [auth A], D [auth A], E [auth A], F [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	2-HYDROXY-3,5-DIIODO-BENZOIC ACID C₇ H₄ I₂ O₃ DHZVWQPHNWDCFS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain T [auth B]	H [auth A], I [auth A], T [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	J [auth A], U [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain S [auth B]	G [auth A], S [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	K [auth A] L [auth A] M [auth A] N [auth A] V [auth B] K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.246
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.41	α = 90
b = 44.8	β = 115.77
c = 146.9	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2018-06-27
Changes: Data collection, Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary