3DLJ

Crystal structure of human carnosine dipeptidase 1

• PDB DOI:  https://doi.org/10.2210/pdb3DLJ/pdb

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


• Deposited: 2008-06-27 Released: 2008-08-19 
• Deposition Author(s): Dong, A., Dobrovetsky, E., Seitova, A., He, H., Tempel, W., Kozieradzki, I., Arrowsmith, C.H., Weigelt, J., Bountra, C., Edwards, A.M., Bochkarev, A., Cossar, D., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Crystal structure of human carnosine dipeptidase 1.

Dobrovetsky, E., Dong, A., Seitova, A., He, H., Tempel, W., Kozieradzki, I., Arrowsmith, C.H., Weigelt, J., Bountra, C., Edwards, A.M., Bochkarev, A., Cossar, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.95 kDa 
• Atom Count: 7,420 
• Modelled Residue Count: 938 
• Deposited Residue Count: 970 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Ala-His dipeptidase	A, B	485	Homo sapiens	Mutation(s): 0  Gene Names: CNDP1, CN1, CPGL2, UNQ1915/PRO4380 EC: 3.4.13.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KN2 (Homo sapiens) Explore Q96KN2  Go to UniProtKB:  Q96KN2
PHAROS:  Q96KN2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.106	α = 90
b = 75.613	β = 109.79
c = 103.716	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Dong, A., Dobrovetsky, E., Seitova, A., He, H., Tempel, W., Kozieradzki, I., Arrowsmith, C.H., Weigelt, J., Bountra, C., Edwards, A.M., Bochkarev, A., Cossar, D., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description