5B29 | pdb_00005b29

The 1.28A structure of human FABP3 F16V mutant complexed with palmitic acid at room temperature

PDB DOI: https://doi.org/10.2210/pdb5B29/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-01-12 Released: 2017-01-18
Deposition Author(s): Matsuoka, D., Sugiyama, S., Kakinouchi, K., Niiyama, M., Murata, M., Matsuoka, S.
Funding Organization(s): JSPS KAKENHI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.199 (Depositor), 0.198 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5B29

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The 1.28A structure of human FABP3 F16V mutant complexed with palmitic acid at room temperature.

Matsuoka, D., Sugiyama, S., Kakinouchi, K., Niiyama, M., Murata, M., Matsuoka, S.

To be published.

Macromolecule Content

Total Structure Weight: 14.96 kDa
Atom Count: 1,324
Modeled Residue Count: 132
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, heart	A	132	Homo sapiens	Mutation(s): 1 Gene Names: FABP3, FABP11, MDGI
UniProt & NIH Common Fund Data Resources
Find proteins for P05413 (Homo sapiens) Explore P05413 Go to UniProtKB: P05413
PHAROS: P05413 GTEx: ENSG00000121769
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05413
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.199 (Depositor), 0.198 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.22	α = 90
b = 71.018	β = 90
c = 34.555	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	24681045
JSPS KAKENHI	Japan	26560436
JSPS KAKENHI	Japan	25650051
JSPS KAKENHI	Japan	25286051

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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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.