5I5R | pdb_00005i5r

Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine

PDB DOI: https://doi.org/10.2210/pdb5I5R/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-15 Released: 2016-03-02
Deposition Author(s): Wright, D.W., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.236 (Depositor), 0.240 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Will be disclosed later

Behr, J.B., Wright, D.W., Hottin, A., Moreno-Vargas, A.J., Robina, I., Davies, G.J.

To be published.

Macromolecule Content

Total Structure Weight: 208.58 kDa
Atom Count: 15,125
Modeled Residue Count: 1,761
Deposited Residue Count: 1,784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase	A, B, C, D	446	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_2970
UniProt
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3I4 Go to UniProtKB: Q8A3I4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A3I4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
68F Query on 68F Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], Q [auth C], T [auth D]	(2S,3S,4R,5S,2'S,3'S,4'R,5'S)-2,2'-(butane-1,4-diyl)bis(5-methylpyrrolidine-3,4-diol) C₁₄ H₂₈ N₂ O₄ FSZVPMVCORPBFY-OPEDVLRTSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], P [auth C], S [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D]