8XAW

Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 1

PDB DOI: https://doi.org/10.2210/pdb8XAW/pdb
EM Map EMD-38205: EMDB EMDataResource
NAKB: 8XAW

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-05 Released: 2024-06-05
Deposition Author(s): An, Q., Deng, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 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

Cryo-EM structure of DUF4297Q53AK55A-HerA-AMPPNP-DNA

An, Q., Deng, Z.

To be published.

Macromolecule Content

Total Structure Weight: 992.2 kDa
Atom Count: 48,983
Modelled Residue Count: 5,913
Deposited Residue Count: 8,272
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding protein	A, B, C, D, E A, B, C, D, E, F	571	Escherichia coli	Mutation(s): 0 Gene Names: CG692_10950
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4297	G, H, I, J, K G, H, I, J, K, L, M, N, O, P, Q, R	394	Escherichia coli	Mutation(s): 0 Gene Names: CG692_10945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
S20DNA1	S	59	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
S20DNA2	T	59	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain W [auth B] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C]	AA [auth D], W [auth B], Y [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain W [auth B] Focus chain Y [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain U [auth A] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain U [auth A]	CA [auth E], EA [auth F], U [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain U [auth A] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth F] Focus chain U [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain FA [auth F] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth C]	BA [auth D] DA [auth E] FA [auth F] V [auth A] X [auth B] BA [auth D], DA [auth E], FA [auth F], V [auth A], X [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C]