8V3O

CCP5 in complex with Glu-P-peptide 1 transition state analog

• PDB DOI: https://doi.org/10.2210/pdb8V3O/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-11-28 Released: 2024-07-17 
• Deposition Author(s): Chen, J., Zehr, E.A., Gruschus, J.M., Szyk, A., Liu, Y., Tanner, M.E., Tjandra, N., Roll-Mecak, A.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Tubulin code eraser CCP5 binds branch glutamates by substrate deformation

Chen, J., Zehr, E.A., Gruschus, J.M., Szyk, A., Liu, Y., Tanner, M.E., Tjandra, N., Roll-Mecak, A.

(2024) Nature 

• DOI: https://doi.org/10.1038/s41586-024-07699-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 61.45 kDa 
• Atom Count: 3,976 
• Modelled Residue Count: 478 
• Deposited Residue Count: 539 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosolic carboxypeptidase-like protein 5	A	524	Homo sapiens	Mutation(s): 1  Gene Names: AGBL5, CCP5 EC: 3.4.17 (PDB Primary Data), 3.4.17.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NDL9 (Homo sapiens) Explore Q8NDL9  Go to UniProtKB:  Q8NDL9
PHAROS:  Q8NDL9 GTEx:  ENSG00000084693

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2A chain	B [auth I]	15	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13885 (Homo sapiens) Explore Q13885  Go to UniProtKB:  Q13885
GTEx:  ENSG00000137267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	D [auth A], E [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.429	α = 90
b = 81.372	β = 90
c = 104	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Chen, J., Zehr, E.A., Gruschus, J.M., Szyk, A., Liu, Y., Tanner, M.E., Tjandra, N., Roll-Mecak, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	1ZIANS003163

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release