9OMM | pdb_00009omm

WrtF fucosyltransferase - tetrasaccharide product

PDB DOI: https://doi.org/10.2210/pdb9OMM/pdb

Classification: TRANSFERASE
Organism(s): Rhizobium tropici CIAT 899
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-14 Released: 2025-10-29
Deposition Author(s): Forrester, T.J.B., Kimber, M.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.265 (Depositor), 0.267 (DCC)
R-Value Work:
0.215 (Depositor), 0.225 (DCC)
R-Value Observed:
0.220 (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

WrtF from Rhizobium tropici CIAT 899 is a GT-A fold fucosyltransferase which binds its donor non-productively

Forrester, T.J.B., Kimber, M.S., Lowary, T.L., Lin, S.

To be published.

Macromolecule Content

Total Structure Weight: 62.42 kDa
Atom Count: 4,190
Modeled Residue Count: 529
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	279	Rhizobium tropici CIAT 899	Mutation(s): 0 Gene Names: GXW80_17485
UniProt
Find proteins for A0A6P1C6J0 (Rhizobium tropici) Explore A0A6P1C6J0 Go to UniProtKB: A0A6P1C6J0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P1C6J0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP (Subject of Investigation/LOI) Query on 5GP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GMP (Subject of Investigation/LOI) Query on GMP Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GUANOSINE C₁₀ H₁₃ N₅ O₅ NYHBQMYGNKIUIF-UUOKFMHZSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
A1CCW (Subject of Investigation/LOI) Query on A1CCW Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-O-acetyl-6-deoxy-alpha-D-talopyranose C₈ H₁₄ O₆ JAMRSAWASNAFCK-FDQSEENZSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
FUC (Subject of Investigation/LOI) Query on FUC Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]