9O4E | pdb_00009o4e

EcAvs2 bound to phage PhiV-1 terminase

PDB DOI: https://doi.org/10.2210/pdb9O4E/pdb
EM Map EMD-70096: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Escherichia coli, Escherichia phage PhiV-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-08 Released: 2026-05-06
Deposition Author(s): Wilkinson, M.E., Gao, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.33 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of phage terminase recognition by the bacterial immune receptor Avs2

Chiu, C., Evans, S.A., Wilkinson, M.E., Li, D., Zhang, F., Gao, A.

To be published.

Macromolecule Content

Total Structure Weight: 965.12 kDa
Atom Count: 52,496
Modeled Residue Count: 6,292
Deposited Residue Count: 8,280
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AVAST type 2 anti-phage system protein Avs2	A, B, C, D	1,484	Escherichia coli	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminase, large subunit	E, F, G, H	586	Escherichia phage PhiV-1	Mutation(s): 0 EC: 3.6.4 (PDB Primary Data), 3.1.21 (PDB Primary Data)
UniProt
Find proteins for A0A7G3WWS0 (Escherichia phage PhiV-1) Explore A0A7G3WWS0 Go to UniProtKB: A0A7G3WWS0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7G3WWS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain O [auth B] SDF format, chain IA [auth H] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain O [auth B] MOL2 format, chain IA [auth H] mmCIF format, chain CA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain O [auth B] mmCIF format, chain IA [auth H]	CA [auth E] EA [auth F] GA [auth G] I [auth A] IA [auth H] CA [auth E], EA [auth F], GA [auth G], I [auth A], IA [auth H], J [auth A], N [auth B], O [auth B], S [auth C], T [auth C], X [auth D], Y [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] SDF format, chain M [auth A] SDF format, chain DA [auth E] SDF format, chain BA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain M [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain M [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain BA [auth D]	AA [auth D] BA [auth D] DA [auth E] FA [auth F] HA [auth G] AA [auth D], BA [auth D], DA [auth E], FA [auth F], HA [auth G], JA [auth H], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]