3FLV | pdb_00003flv

The crystal structure of human acyl-CoenzymeA binding domain containing 5

• PDB DOI: https://doi.org/10.2210/pdb3FLV/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-12-19 Released: 2009-02-03 
• Deposition Author(s): Ugochukwu, E., Roos, A., Yue, W.W., Shafqat, N., Salah, E., Savitsky, P., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.259 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of human acyl-Coenzyme A binding domain containing 5

Ugochukwu, E., Roos, A., Yue, W.W., Shafqat, N., Salah, E., Savitsky, P., Muniz, J.R.C., von Delft, F., Oppermann, U.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.67 kDa 
• Atom Count: 1,686 
• Modeled Residue Count: 181 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA-binding domain-containing protein 5	A, B	119	Homo sapiens	Mutation(s): 0  Gene Names: ACBD5, KIAA1996 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T8D3 (Homo sapiens) Explore Q5T8D3  Go to UniProtKB:  Q5T8D3
PHAROS:  Q5T8D3 GTEx:  ENSG00000107897

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	D [auth A], E [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
STE	C [auth A]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
UNX	F [auth B], G [auth B], H [auth B], I [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.259 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.751	α = 90
b = 34.064	β = 102.16
c = 54.877	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Ugochukwu, E., Roos, A., Yue, W.W., Shafqat, N., Salah, E., Savitsky, P., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description