6YPA

The C146A variant of an amidase from Pyrococcus horikoshii with bound glutaramide

• PDB DOI: https://doi.org/10.2210/pdb6YPA/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-04-15 Released: 2020-06-03 
• Deposition Author(s): Sewell, B.T., Su, S., Venter, P., Makumire, S.
• Funding Organization(s): Global Challenges Research Fund

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.240 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7OVG

Literature

The structure of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide suggests the basis of amide recognition.

Sewell, B.T., Su, S., Venter, P., Makumire, S.

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 Evidence: gel filtration

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)

Macromolecule Content

• Total Structure Weight: 128.55 kDa 
• Atom Count: 9,115 
• Modelled Residue Count: 1,059 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CN hydrolase domain-containing protein	A, B, C, D	282	Pyrococcus horikoshii	Mutation(s): 1  Gene Names: PH0642
UniProt
Find proteins for O58376 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58376  Go to UniProtKB:  O58376

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6W (Subject of Investigation/LOI)	E [auth A], G [auth B], H [auth C], I [auth D]	pentanediamide C5 H10 N2 O2 RCCYSVYHULFYHE-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.240 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.684	α = 90
b = 100.639	β = 90
c = 134.096	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Sewell, B.T., Su, S., Venter, P., Makumire, S.

---

Funding Organization	Location	Grant Number
Global Challenges Research Fund	United Kingdom	ST/R002754/1

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description