8OUG | pdb_00008oug

Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus

PDB DOI: https://doi.org/10.2210/pdb8OUG/pdb

Classification: HYDROLASE
Organism(s): Thermococcus chitonophagus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-22 Released: 2024-05-01
Deposition Author(s): Rypniewski, W., Biniek-Antosiak, K., Bejger, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.165 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus

Rypniewski, W., Biniek-Antosiak, K., Bejger, M.

To be published.

Macromolecule Content

Total Structure Weight: 92.92 kDa
Atom Count: 6,769
Modeled Residue Count: 780
Deposited Residue Count: 781
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	781	Thermococcus chitonophagus	Mutation(s): 0 Gene Names: A3L04_10820 EC: 3.2.1.23
UniProt
Find proteins for A0A160VTD9 (Thermococcus chitonophagus) Explore A0A160VTD9 Go to UniProtKB: A0A160VTD9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A160VTD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain CA [auth A] SDF format, chain C [auth A] SDF format, chain BA [auth A] SDF format, chain B [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain B [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain B [auth A] mmCIF format, chain AA [auth A]	AA [auth A] B [auth A] BA [auth A] C [auth A] CA [auth A] AA [auth A], B [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain DA [auth A]	DA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]