Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 343.74 kDa 
• Atom Count: 24224 
• Residue Count: 2892 
• Unique protein chains: 1

1XFD

Structure of a human A-type Potassium Channel Accelerating factor DPPX, a member of the dipeptidyl aminopeptidase family

• DOI: 10.2210/pdb1XFD/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2004-09-14 Released: 2004-10-26 
• Deposition Author(s): Strop, P., Bankovich, A.J., Hansen, K.C., Garcia, K.C., Brunger, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 

Literature

Structure of a human A-type potassium channel interacting protein DPPX, a member of the dipeptidyl aminopeptidase family

Strop, P., Bankovich, A.J., Hansen, K.C., Garcia, K.C., Brunger, A.T.

(2004) J Mol Biol 343: 1055-1065

• PubMed: 15476821 
• DOI: 10.1016/j.jmb.2004.09.003
• Primary Citation of Related Structures:  
  1XFD


• PubMed Abstract: 
  

It has recently been reported that dipeptidyl aminopeptidase X (DPPX) interacts with the voltage-gated potassium channel Kv4 and that co-expression of DPPX together with Kv4 pore forming alpha-subunits, and potassium channel interacting proteins (KChIPs), reconstitutes properties of native A-type potassium channels in vitro. Here we report the X-ray crystal structure of the extracellular domain of human DPPX determined at 3.0A resolution. This structure reveals the potential for a surface electrostatic change based on the protonation state of histidine. Subtle changes in extracellular pH might modulate the interaction of DPPX with Kv4.2 and possibly with other proteins. We propose models of DPPX interaction with the voltage-gated potassium channel complex. The dimeric structure of DPPX is highly homologous to the related protein DPP-IV. Comparison of the active sites of DPPX and DPP-IV reveals loss of the catalytic serine residue but the presence of an additional serine near the "active" site. However, the arrangement of residues is inconsistent with that of canonical serine proteases and DPPX is unlikely to function as a protease (dipeptidyl aminopeptidase).

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford University, James H. Clark Center E300, 318 Campus Drive, Stanford, CA 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl aminopeptidase-like protein 6	A, B, C, D	723	Homo sapiens	Mutation(s): 0  Gene Names: DPPX, DPP6
Find proteins for P42658 (Homo sapiens) Explore P42658  Go to UniProtKB:  P42658
NIH Common Fund Data Resources
PHAROS:  P42658 GTEx:  ENSG00000130226

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, K, N, Q, T, V, Y, Z	3		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	4		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, M, O, P, S, U	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, R, W	3		N-Glycosylation

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	X	4		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.98	α = 90
b = 170.23	β = 92.11
c = 159.316	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-14 
• Released Date: 2004-10-26 
Deposition Author(s): Strop, P., Bankovich, A.J., Hansen, K.C., Garcia, K.C., Brunger, A.T.

Revision History 

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary