2OME | pdb_00002ome

Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)

• PDB DOI: https://doi.org/10.2210/pdb2OME/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-22 Released: 2007-02-06 
• Deposition Author(s): Pilka, E.S., Guo, K., Rojkova, A., Debreczeni, J.E., Kavanagh, K.L., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)

Pilka, E.S., Guo, K., Rojkova, A., Debreczeni, J.E., Kavanagh, K.L., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Oppermann, U.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 303.5 kDa 
• Atom Count: 20,793 
• Modeled Residue Count: 2,640 
• Deposited Residue Count: 2,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal-binding protein 2	A, B, C, D, E, F, G, H	336	Homo sapiens	Mutation(s): 0  Gene Names: CTBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P56545 (Homo sapiens) Explore P56545  Go to UniProtKB:  P56545
PHAROS:  P56545 GTEx:  ENSG00000175029

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.754	α = 90
b = 141.574	β = 98.93
c = 138.215	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Pilka, E.S., Guo, K., Rojkova, A., Debreczeni, J.E., Kavanagh, K.L., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description