5INR | pdb_00005inr

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.182 (Depositor), 0.180 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 267.77 kDa
Atom Count: 21,438
Modeled Residue Count: 2,305
Deposited Residue Count: 2,345
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRO Query on PRO Download Ideal Coordinates CCD File SDF format, chain YA [auth E] SDF format, chain Y [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain GA [auth C] MOL2 format, chain YA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain GA [auth C] mmCIF format, chain YA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain GA [auth C]	GA [auth C], OA [auth D], P [auth A], Y [auth B], YA [auth E]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain GA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Y [auth B] Focus chain YA [auth E] Interactions & Density Focus chain GA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Y [auth B] Focus chain YA [auth E]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain XA [auth E] SDF format, chain X [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain FA [auth C] MOL2 format, chain XA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain XA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain FA [auth C]	FA [auth C], NA [auth D], O [auth A], X [auth B], XA [auth E]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain FA [auth C] Focus chain NA [auth D] Focus chain O [auth A] Focus chain X [auth B] Focus chain XA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain NA [auth D] Focus chain O [auth A] Focus chain X [auth B] Focus chain XA [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain W [auth B] SDF format, chain VA [auth E] SDF format, chain V [auth B] SDF format, chain UA [auth E] SDF format, chain U [auth B] SDF format, chain TA [auth E] SDF format, chain T [auth B] SDF format, chain SA [auth E] SDF format, chain S [auth B] SDF format, chain RA [auth E] SDF format, chain R [auth B] SDF format, chain QA [auth E] SDF format, chain Q [auth B] SDF format, chain PA [auth E] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] 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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain WA [auth E] MOL2 format, chain WA [auth E] mmCIF format, chain WA [auth E]	WA [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain WA [auth E] Interactions & Density Focus chain WA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.182 (Depositor), 0.180 (DCC)
R-Value Work: 0.159 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

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

View Full Validation Report

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