5INR

A C69-family cysteine dipeptidase in complex with Ala-Pro from Lactobacillus farciminis

• PDB DOI: https://doi.org/10.2210/pdb5INR/pdb

• Classification: HYDROLASE
• Organism(s): Companilactobacillus farciminis KCTC 3681 = DSM 20184
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2017-03-15 
• Deposition Author(s): Kono, R., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.182 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation

Kono, R., Watanabe, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content

• Total Structure Weight: 267.77 kDa 
• Atom Count: 21,438 
• Modelled Residue Count: 2,305 
• Deposited Residue Count: 2,345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidase	A, B, C, D, E	469	Companilactobacillus farciminis KCTC 3681 = DSM 20184	Mutation(s): 0  Gene Names: FC68_GL001211

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO	GA [auth C], OA [auth D], P [auth A], Y [auth B], YA [auth E]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
ALA	FA [auth C], NA [auth D], O [auth A], X [auth B], XA [auth E]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
EDO	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], G [auth A], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	WA [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.182 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.398	α = 90
b = 182.299	β = 112.84
c = 98.335	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Kono, R., Watanabe, K.

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description