9V0Y | pdb_00009v0y

Helical structure of KomBC in complex with dITP and NAM

PDB DOI: https://doi.org/10.2210/pdb9V0Y/pdb
EM Map EMD-64676: EMDB EMDataResource

Classification: CELL INVASION
Organism(s): Archangium gephyra
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-19 Released: 2025-12-17
Deposition Author(s): Li, Y., Zheng, Q., Li, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.64 Å
Aggregation State: PARTICLE
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Helical structure of KomBC in complex with dITP and NAM

Li, Y., Zheng, Q., Li, S.

To be published.

Macromolecule Content

Total Structure Weight: 416.5 kDa
Atom Count: 29,096
Modeled Residue Count: 3,656
Deposited Residue Count: 3,672
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthosine/inosine triphosphate pyrophosphatase	A [auth C] B [auth F] C [auth I] D [auth L] E [auth a] A [auth C], B [auth F], C [auth I], D [auth L], E [auth a], F [auth d], K [auth o], L [auth r]	181	Archangium gephyra	Mutation(s): 0 Gene Names: AA314_06977
UniProt
Find proteins for A0AAC8QDB0 (Archangium gephyra) Explore A0AAC8QDB0 Go to UniProtKB: A0AAC8QDB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAC8QDB0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase	G [auth g] H [auth h] I [auth i] J [auth j] M [auth s] G [auth g], H [auth h], I [auth i], J [auth j], M [auth s], N [auth t], O [auth u], P [auth v]	278	Archangium gephyra	Mutation(s): 0 Gene Names: AA314_06978
UniProt
Find proteins for A0AAC8TGL7 (Archangium gephyra) Explore A0AAC8TGL7 Go to UniProtKB: A0AAC8TGL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAC8TGL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 AA [auth d] SDF format, chain GA [auth o] SDF format, chain IA [auth r] SDF format, chain Q [auth C] SDF format, chain S [auth F] SDF format, chain U [auth I] SDF format, chain W [auth L] SDF format, chain Y [auth a] MOL2 format, chain AA [auth d] MOL2 format, chain GA [auth o] MOL2 format, chain IA [auth r] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth F] MOL2 format, chain U [auth I] MOL2 format, chain W [auth L] MOL2 format, chain Y [auth a] mmCIF format, chain AA [auth d] mmCIF format, chain GA [auth o] mmCIF format, chain IA [auth r] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth F] mmCIF format, chain U [auth I] mmCIF format, chain W [auth L] mmCIF format, chain Y [auth a]	AA [auth d] GA [auth o] IA [auth r] Q [auth C] S [auth F] AA [auth d], GA [auth o], IA [auth r], Q [auth C], S [auth F], U [auth I], W [auth L], Y [auth a]	2'-deoxyinosine 5'-triphosphate C₁₀ H₁₅ N₄ O₁₃ P₃ UFJPAQSLHAGEBL-RRKCRQDMSA-N		Interactions Focus chain AA [auth d] Focus chain GA [auth o] Focus chain IA [auth r] Focus chain Q [auth C] Focus chain S [auth F] Focus chain U [auth I] Focus chain W [auth L] Focus chain Y [auth a] Interactions & Density Focus chain AA [auth d] Focus chain GA [auth o] Focus chain IA [auth r] Focus chain Q [auth C] Focus chain S [auth F] Focus chain U [auth I] Focus chain W [auth L] Focus chain Y [auth a]
NCA (Subject of Investigation/LOI) Query on NCA Download Ideal Coordinates CCD File SDF format, chain CA [auth g] SDF format, chain DA [auth h] SDF format, chain EA [auth i] SDF format, chain FA [auth j] SDF format, chain KA [auth s] SDF format, chain LA [auth t] SDF format, chain MA [auth u] SDF format, chain NA [auth v] MOL2 format, chain CA [auth g] MOL2 format, chain DA [auth h] MOL2 format, chain EA [auth i] MOL2 format, chain FA [auth j] MOL2 format, chain KA [auth s] MOL2 format, chain LA [auth t] MOL2 format, chain MA [auth u] MOL2 format, chain NA [auth v] mmCIF format, chain CA [auth g] mmCIF format, chain DA [auth h] mmCIF format, chain EA [auth i] mmCIF format, chain FA [auth j] mmCIF format, chain KA [auth s] mmCIF format, chain LA [auth t] mmCIF format, chain MA [auth u] mmCIF format, chain NA [auth v]	CA [auth g] DA [auth h] EA [auth i] FA [auth j] KA [auth s] CA [auth g], DA [auth h], EA [auth i], FA [auth j], KA [auth s], LA [auth t], MA [auth u], NA [auth v]	NICOTINAMIDE C₆ H₆ N₂ O DFPAKSUCGFBDDF-UHFFFAOYSA-N		Interactions Focus chain CA [auth g] Focus chain DA [auth h] Focus chain EA [auth i] Focus chain FA [auth j] Focus chain KA [auth s] Focus chain LA [auth t] Focus chain MA [auth u] Focus chain NA [auth v] Interactions & Density Focus chain CA [auth g] Focus chain DA [auth h] Focus chain EA [auth i] Focus chain FA [auth j] Focus chain KA [auth s] Focus chain LA [auth t] Focus chain MA [auth u] Focus chain NA [auth v]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth d] SDF format, chain HA [auth o] SDF format, chain JA [auth r] SDF format, chain R [auth C] SDF format, chain T [auth F] SDF format, chain V [auth I] SDF format, chain X [auth L] SDF format, chain Z [auth a] MOL2 format, chain BA [auth d] MOL2 format, chain HA [auth o] MOL2 format, chain JA [auth r] MOL2 format, chain R [auth C] MOL2 format, chain T [auth F] MOL2 format, chain V [auth I] MOL2 format, chain X [auth L] MOL2 format, chain Z [auth a] mmCIF format, chain BA [auth d] mmCIF format, chain HA [auth o] mmCIF format, chain JA [auth r] mmCIF format, chain R [auth C] mmCIF format, chain T [auth F] mmCIF format, chain V [auth I] mmCIF format, chain X [auth L] mmCIF format, chain Z [auth a]	BA [auth d] HA [auth o] JA [auth r] R [auth C] T [auth F] BA [auth d], HA [auth o], JA [auth r], R [auth C], T [auth F], V [auth I], X [auth L], Z [auth a]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth d] Focus chain HA [auth o] Focus chain JA [auth r] Focus chain R [auth C] Focus chain T [auth F] Focus chain V [auth I] Focus chain X [auth L] Focus chain Z [auth a] Interactions & Density Focus chain BA [auth d] Focus chain HA [auth o] Focus chain JA [auth r] Focus chain R [auth C] Focus chain T [auth F] Focus chain V [auth I] Focus chain X [auth L] Focus chain Z [auth a]