5INX | pdb_00005inx

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

PDB DOI: https://doi.org/10.2210/pdb5INX/pdb

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

Deposited: 2016-03-08 Released: 2017-03-15
Deposition Author(s): Kono, R., Watanabe, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.180 (Depositor), 0.181 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 265.71 kDa
Atom Count: 21,315
Modeled Residue Count: 2,305
Deposited Residue Count: 2,345
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MET Query on MET Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D], N [auth E]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.180 (Depositor), 0.181 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.65	α = 90
b = 182.415	β = 112.75
c = 98.215	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Kono, R.

Watanabe, K.

Revision History (Full details and data files)

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
Version 1.3: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary