9IR0 | pdb_00009ir0

phage HY126 glycosyltransferase with UDP

PDB DOI: https://doi.org/10.2210/pdb9IR0/pdb

Classification: TRANSFERASE
Organism(s): Phage #D
Expression System: Escherichia
Mutation(s): No

Deposited: 2024-07-13 Released: 2025-07-16
Deposition Author(s): Yu, H., Lianrong, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.203 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
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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

Structure of phage HY126 glycosyltransferase protein at 2.46 angstroms resolution

Yu, H.

To be published.

Macromolecule Content

Total Structure Weight: 84.3 kDa
Atom Count: 6,234
Modeled Residue Count: 734
Deposited Residue Count: 738
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 subfamily 4-like N-terminal domain-containing protein	A, B	369	Phage #D	Mutation(s): 0 Gene Names: FFEPELFE_00237
UniProt
Find proteins for Q7Y5D5 (Escherichia phage RB69) Explore Q7Y5D5 Go to UniProtKB: Q7Y5D5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Y5D5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.203 (Depositor), 0.202 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.62	α = 90
b = 94.97	β = 90
c = 152.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.