9VDO | pdb_00009vdo

Cryo-EM structure of the substrate bound DRT4

PDB DOI: https://doi.org/10.2210/pdb9VDO/pdb
NAKB: 9VDO
EM Map EMD-64990: EMDB EMDataResource

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

Deposited: 2025-06-09 Released: 2025-11-12
Deposition Author(s): Wang, Y., Deng, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.93 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 the substrate bound DRT4

Wang, Y., Deng, Z.

To be published.

Macromolecule Content

Total Structure Weight: 395.62 kDa
Atom Count: 25,026
Modeled Residue Count: 2,994
Deposited Residue Count: 3,324
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase domain-containing protein	A C [auth B] E [auth D] G [auth F] I [auth H] A, C [auth B], E [auth D], G [auth F], I [auth H], K	549	Escherichia coli	Mutation(s): 0 Gene Names: BZ227_14395
UniProt
Find proteins for A0A628R156 (Salmonella muenchen) Explore A0A628R156 Go to UniProtKB: A0A628R156
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A628R156
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PCPCPCPAP*A)-3')	B [auth I] D [auth C] F [auth E] H [auth G] J B [auth I], D [auth C], F [auth E], H [auth G], J, L	5	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCP (Subject of Investigation/LOI) Query on DCP Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain V [auth F] SDF format, chain S [auth D] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain BA [auth K] MOL2 format, chain Y [auth H] MOL2 format, chain V [auth F] MOL2 format, chain S [auth D] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth K] mmCIF format, chain Y [auth H] mmCIF format, chain V [auth F] mmCIF format, chain S [auth D] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth K]	BA [auth K] M [auth A] P [auth B] S [auth D] V [auth F] BA [auth K], M [auth A], P [auth B], S [auth D], V [auth F], Y [auth H]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ RGWHQCVHVJXOKC-SHYZEUOFSA-N		Interactions Focus chain BA [auth K] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth D] Focus chain V [auth F] Focus chain Y [auth H] Interactions & Density Focus chain BA [auth K] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth D] Focus chain V [auth F] Focus chain Y [auth H]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain DA [auth K] SDF format, chain CA [auth K] SDF format, chain AA [auth H] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth K] MOL2 format, chain AA [auth H] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth K] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth K] DA [auth K] N [auth A] O [auth A] AA [auth H], CA [auth K], DA [auth K], N [auth A], O [auth A], Q [auth B], R [auth B], T [auth D], U [auth D], W [auth F], X [auth F], Z [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth H]