5Y5C | pdb_00005y5c

Crystal structure of dha bind to bovine beta-lactoglobulin

PDB DOI: https://doi.org/10.2210/pdb5Y5C/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2017-08-08 Released: 2018-08-08
Deposition Author(s): Jiang, L., Liu, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.244 (Depositor), 0.243 (DCC)
R-Value Work:
0.200 (Depositor), 0.205 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of dha bind to bovine beta-lactoglobulin

Jiang, L., Liu, J.

To be published.

Macromolecule Content

Total Structure Weight: 37.26 kDa
Atom Count: 2,531
Modeled Residue Count: 317
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactoglobulin	A, B	162	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P02754 (Bos taurus) Explore P02754 Go to UniProtKB: P02754
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02754
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HXA (Subject of Investigation/LOI) Query on HXA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID C₂₂ H₃₂ O₂ MBMBGCFOFBJSGT-KUBAVDMBSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.244 (Depositor), 0.243 (DCC)
R-Value Work: 0.200 (Depositor), 0.205 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.49	α = 90
b = 52.49	β = 90
c = 108.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.