9IQW | pdb_00009iqw

phage HY126 encoded D-arabinose 1,5-diphosphate phosphatase AfhF

PDB DOI: https://doi.org/10.2210/pdb9IQW/pdb

Classification: VIRAL PROTEIN
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: 1.64 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.175 (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 bisphosphate phosphatase at 1.64 angstroms resolution

Yu, H.

To be published.

Macromolecule Content

Total Structure Weight: 62.09 kDa
Atom Count: 5,000
Modeled Residue Count: 510
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsule biosynthesis protein	A, B, C, D [auth E]	134	Phage #D	Mutation(s): 0 Gene Names: mogra_227
UniProt
Find proteins for Q7Y587 (Escherichia phage RB69) Explore Q7Y587 Go to UniProtKB: Q7Y587
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Y587
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth E] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth E] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], L [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth E] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]