5L78 | pdb_00005l78

Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain (in NAD+ bound form)

• PDB DOI: https://doi.org/10.2210/pdb5L78/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-06-02 Released: 2017-05-10 
• Deposition Author(s): Kopec, J., Pena, I.A., Rembeza, E., Strain-Damerell, C., Chalk, R., Borkowska, O., Goubin, S., Velupillai, S., Burgess-Brown, N., Arrowsmith, C., Edwards, A., Bountra, C., Arruda, P., Yue, W.W.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain (in NAD+ bound form)

Kopec, J., Yue, W.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 110.76 kDa 
• Atom Count: 6,833 
• Modeled Residue Count: 871 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-aminoadipic semialdehyde synthase, mitochondrial	A, B	497	Homo sapiens	Mutation(s): 0  Gene Names: AASS EC: 1.5.1.8 (PDB Primary Data), 1.5.1.9 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UDR5 (Homo sapiens) Explore Q9UDR5  Go to UniProtKB:  Q9UDR5
PHAROS:  Q9UDR5 GTEx:  ENSG00000008311

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.222	α = 90
b = 86.633	β = 90
c = 149.924	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Kopec, J., Pena, I.A., Rembeza, E., Strain-Damerell, C., Chalk, R., Borkowska, O., Goubin, S., Velupillai, S., Burgess-Brown, N., Arrowsmith, C., Edwards, A., Bountra, C., Arruda, P., Yue, W.W.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary