3AKM

X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue

PDB DOI: https://doi.org/10.2210/pdb3AKM/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-07-14 Released: 2011-07-20
Deposition Author(s): Wielens, J., Laguerre, A.J.K., Parker, M.W., Scanlon, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.279
R-Value Work: 0.226
R-Value Observed: 0.229

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of human and rat intestinal fatty acid binding proteins in complex with 11-(Dansylamino)undecanoic acid

Laguerre, A.J.K., Wielens, J., Parker, M.W., Porter, C.J., Scanlon, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 62.23 kDa
Atom Count: 4,463
Modelled Residue Count: 524
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, intestinal	A, B, C, D	131	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P12104 (Homo sapiens) Explore P12104 Go to UniProtKB: P12104
PHAROS: P12104 GTEx: ENSG00000145384
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12104
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
11D Query on 11D Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid C₂₃ H₃₄ N₂ O₄ S CEPGVMDMVJGHFQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
11D	BindingDB: 3AKM	Ki: 300 (nM) from 1 assay(s)
		Kd: 360 (nM) from 1 assay(s)
		-TΔS: 9.96 (kJ/mol) from 1 assay(s)
		ΔH: -4.81e+1 (kJ/mol) from 1 assay(s)
		ΔG: -3.83e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.279
R-Value Work: 0.226
R-Value Observed: 0.229
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.02	α = 90
b = 79.011	β = 94.48
c = 63.24	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3AKM

X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue

Crystal structures of human and rat intestinal fatty acid binding proteins in complex with 11-(Dansylamino)undecanoic acid

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)