9U3A | pdb_00009u3a

Glycogen phosphorylase from Segatella copri in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb9U3A/pdb
EM Map EMD-63814: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Segatella copri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-18 Released: 2026-02-18
Deposition Author(s): Shobu, K., Fukuda, Y., Inoue, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural and mechanistic diversity of glycogen phosphorylase from gut bacteria

Shobu, K., Takai, M., Fukuda, Y., Inoue, T.

To be published.

Macromolecule Content

Total Structure Weight: 496.76 kDa
Atom Count: 34,954
Modeled Residue Count: 4,260
Deposited Residue Count: 4,260
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-glucan family phosphorylase	A, B, C, D, E	852	Segatella copri	Mutation(s): 0 Gene Names: glgP, DW064_01070, LYY06_13165
UniProt
Find proteins for A0AA93BMC9 (Segatella copri) Explore A0AA93BMC9 Go to UniProtKB: A0AA93BMC9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA93BMC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth E] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth E] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth B] I [auth B] J [auth D] F [auth A], G [auth A], H [auth B], I [auth B], J [auth D], K [auth D], L [auth E], M [auth E]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E]