9XVC | pdb_00009xvc

Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments

PDB DOI: https://doi.org/10.2210/pdb9XVC/pdb
EM Map EMD-67286: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-11-26 Released: 2026-01-21
Deposition Author(s): Xie, W., Feng, H., Luo, M.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments

Xie, W., Feng, H., Luo, M.

To be published.

Macromolecule Content

Total Structure Weight: 419.2 kDa
Atom Count: 29,400
Modeled Residue Count: 3,568
Deposited Residue Count: 3,584
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase	A [auth C] B [auth D] G [auth A] H [auth B] I [auth K] A [auth C], B [auth D], G [auth A], H [auth B], I [auth K], J [auth L], O [auth I], P [auth J]	184	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KomC(H146N), a SIR2-domain NADase	C [auth H] D [auth G] E [auth F] F [auth E] K [auth P] C [auth H], D [auth G], E [auth F], F [auth E], K [auth P], L [auth O], M [auth N], N [auth M]	264	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y43 (Subject of Investigation/LOI) Query on Y43 Download Ideal Coordinates CCD File SDF format, chain EA [auth I] SDF format, chain FA [auth J] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth K] SDF format, chain Z [auth L] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth L] mmCIF format, chain EA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain W [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth L]	EA [auth I] FA [auth J] Q [auth C] R [auth D] W [auth A] EA [auth I], FA [auth J], Q [auth C], R [auth D], W [auth A], X [auth B], Y [auth K], Z [auth L]	2'-deoxyinosine 5'-triphosphate C₁₀ H₁₅ N₄ O₁₃ P₃ UFJPAQSLHAGEBL-RRKCRQDMSA-N		Interactions Focus chain EA [auth I] Focus chain FA [auth J] Focus chain Q [auth C] Focus chain R [auth D] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain EA [auth I] Focus chain FA [auth J] Focus chain Q [auth C] Focus chain R [auth D] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth K] Focus chain Z [auth L]
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain AA [auth P] SDF format, chain BA [auth O] SDF format, chain CA [auth N] SDF format, chain DA [auth M] SDF format, chain S [auth H] SDF format, chain T [auth G] SDF format, chain U [auth F] SDF format, chain V [auth E] MOL2 format, chain AA [auth P] MOL2 format, chain BA [auth O] MOL2 format, chain CA [auth N] MOL2 format, chain DA [auth M] MOL2 format, chain S [auth H] MOL2 format, chain T [auth G] MOL2 format, chain U [auth F] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth P] mmCIF format, chain BA [auth O] mmCIF format, chain CA [auth N] mmCIF format, chain DA [auth M] mmCIF format, chain S [auth H] mmCIF format, chain T [auth G] mmCIF format, chain U [auth F] mmCIF format, chain V [auth E]	AA [auth P] BA [auth O] CA [auth N] DA [auth M] S [auth H] AA [auth P], BA [auth O], CA [auth N], DA [auth M], S [auth H], T [auth G], U [auth F], V [auth E]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain AA [auth P] Focus chain BA [auth O] Focus chain CA [auth N] Focus chain DA [auth M] Focus chain S [auth H] Focus chain T [auth G] Focus chain U [auth F] Focus chain V [auth E] Interactions & Density Focus chain AA [auth P] Focus chain BA [auth O] Focus chain CA [auth N] Focus chain DA [auth M] Focus chain S [auth H] Focus chain T [auth G] Focus chain U [auth F] Focus chain V [auth E]