9DBJ | pdb_00009dbj

Structure of Hailong HalB R164A mutant with non-hydrolyzable dATP

PDB DOI: https://doi.org/10.2210/pdb9DBJ/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Rhodobacteraceae bacterium QY30
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-23 Released: 2025-05-07
Deposition Author(s): Tan, J.M.J., Melamed, S., Cofsky, J.C., Hobbs, S.J., Kruse, A.C., Sorek, R., Kranzusch, P.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 ?
R-Value Free:
0.239 (Depositor), 0.234 (DCC)
R-Value Work:
0.207 (Depositor), 0.205 (DCC)
R-Value Observed:
0.208 (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

A DNA-gated molecular guard controls bacterial Hailong anti-phage defense

Tan, J.M.J., Melamed, S., Cofsky, J.C., Hobbs, S.J., Kruse, A.C., Sorek, R., Kranzusch, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 160.14 kDa
Atom Count: 11,025
Modelled Residue Count: 1,298
Deposited Residue Count: 1,374
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HalB	A, B, C, D, E A, B, C, D, E, F	229	Rhodobacteraceae bacterium QY30	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A3G (Subject of Investigation/LOI) Query on A1A3G Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(2R)-3-(4-{[(S)-{[(2R,3R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}phenyl)-2-{[(2R)-pyrrolidine-2-carbonyl]amino}propanoic acid (non-preferred name) C₂₄ H₃₀ N₇ O₉ P FVPBNOZKHKXLRZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
A1A3H (Subject of Investigation/LOI) Query on A1A3H Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	(2R)-2-amino-3-(4-{[(R)-{[(2R,3R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}phenyl)propanoic acid (non-preferred name) C₁₉ H₂₃ N₆ O₈ P FVTPNOGUOYZKIO-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
F2A (Subject of Investigation/LOI) Query on F2A Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain S [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain S [auth D]	H [auth A] K [auth B] O [auth C] S [auth D] V [auth E] H [auth A], K [auth B], O [auth C], S [auth D], V [auth E], Y [auth F]	2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine C₁₁ H₁₈ N₅ O₁₁ P₃ XETARULVTCYJAN-XLPZGREQSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
D5M (Subject of Investigation/LOI) Query on D5M Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₆ P KHWCHTKSEGGWEX-RRKCRQDMSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Z [auth F] SDF format, chain L [auth B] SDF format, chain T [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D]	AA [auth F] I [auth A] J [auth A] L [auth B] M [auth B] AA [auth F], I [auth A], J [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], W [auth E], X [auth E], Z [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F]