1XG5 | pdb_00001xg5

Structure of human putative dehydrogenase MGC4172 in complex with NADP

• PDB DOI: https://doi.org/10.2210/pdb1XG5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-16 Released: 2004-10-05 
• Deposition Author(s): Kavanagh, K., Ng, S., Sharma, S., Vedadi, M., von Delft, F., Walker, J.R., dhe Paganon, S., Bray, J., Oppermann, U., Edwards, A., Arrowsmith, C., Sundstrom, M., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structural Genomics Consortium: Structure of the putative human dehydrogenase MGC4172

Kavanagh, K., Ng, S., Sharma, S., Vedadi, M., von Delft, F., Walker, J.R., dhe Paganon, S., Bray, J., Oppermann, U., Edwards, A., Arrowsmith, C., Sundstrom, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 125.02 kDa 
• Atom Count: 8,763 
• Modeled Residue Count: 1,012 
• Deposited Residue Count: 1,116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARPG836	A, B, C, D	279	Homo sapiens	Mutation(s): 0  Gene Names: MGC4172 EC: 1.1.1.270 (UniProt), 1.1.1.62 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UWP2 (Homo sapiens) Explore Q6UWP2  Go to UniProtKB:  Q6UWP2
PHAROS:  Q6UWP2 GTEx:  ENSG00000278535

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], G [auth B], H [auth C], J [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ACY	F [auth A], I [auth C], K [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.71	α = 90
b = 124.669	β = 97.23
c = 75.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Kavanagh, K., Ng, S., Sharma, S., Vedadi, M., von Delft, F., Walker, J.R., dhe Paganon, S., Bray, J., Oppermann, U., Edwards, A., Arrowsmith, C., Sundstrom, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description