5L78

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

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

Kopec, J., Yue, W.W.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UDR5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	F [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

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