8U01 | pdb_00008u01

Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius

PDB DOI: https://doi.org/10.2210/pdb8U01/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola plebeius
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-28 Released: 2023-09-27
Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius

Kim, Y., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 107.26 kDa
Atom Count: 7,627
Modeled Residue Count: 909
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 2, sugar binding domain protein	A	916	Phocaeicola plebeius	Mutation(s): 0 Gene Names: BACPLE_01374 EC: 3.2.1.23
UniProt
Find proteins for B5CXD3 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CXD3 Go to UniProtKB: B5CXD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5CXD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain LA [auth A] MOL2 format, chain LA [auth A] mmCIF format, chain LA [auth A]	LA [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Interactions & Density Focus chain LA [auth A]
TAG (Subject of Investigation/LOI) Query on TAG Download Ideal Coordinates CCD File SDF format, chain NA [auth A] MOL2 format, chain NA [auth A] mmCIF format, chain NA [auth A]	NA [auth A]	D-tagatose C₆ H₁₂ O₆ BJHIKXHVCXFQLS-PQLUHFTBSA-N		Interactions Focus chain NA [auth A] Interactions & Density Focus chain NA [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain OA [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	BA [auth A] J [auth A] K [auth A] L [auth A] M [auth A] BA [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth A], OA [auth A], T [auth A], U [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain OA [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain BA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain OA [auth A] Focus chain T [auth A] Focus chain U [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain KA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth A]	G [auth A], H [auth A], I [auth A], KA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] CA [auth A] DA [auth A] EA [auth A] FA [auth A] AA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [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 CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [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 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 CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [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 W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth A] SDF format, chain V [auth A] MOL2 format, chain F [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] mmCIF format, chain F [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A]	F [auth A], S [auth A], V [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain S [auth A] Focus chain V [auth A] Interactions & Density Focus chain F [auth A] Focus chain S [auth A] Focus chain V [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]