8PMK | pdb_00008pmk

Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) complex with prFMN bound

PDB DOI: https://doi.org/10.2210/pdb8PMK/pdb
EM Map EMD-17762: EMDB EMDataResource

Classification: FLAVOPROTEIN
Organism(s): Thauera chlorobenzoica
Expression System: Thauera chlorobenzoica
Mutation(s): No

Deposited: 2023-06-28 Released: 2024-07-10
Deposition Author(s): Kayastha, K., Ermler, U.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.43 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

Active Pcd complex with prFMN bound

Kayastha, K., Ermler, U.

To be published.

Macromolecule Content

Total Structure Weight: 358.41 kDa
Atom Count: 23,958
Modeled Residue Count: 3,012
Deposited Residue Count: 3,162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phthaloyl-CoA decarboxylase	A, B, C, D, E A, B, C, D, E, F	527	Thauera chlorobenzoica	Mutation(s): 0 Gene Names: Tchl_3080
UniProt
Find proteins for A0A193DUB4 (Thauera chlorobenzoica) Explore A0A193DUB4 Go to UniProtKB: A0A193DUB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A193DUB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BYN (Subject of Investigation/LOI) Query on BYN Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	AA [auth E] FA [auth F] G [auth A] L [auth B] Q [auth C] AA [auth E], FA [auth F], G [auth A], L [auth B], Q [auth C], V [auth D]	hydroxylated prenyl-FMN C₂₂ H₃₁ N₄ O₁₀ P BDNVCRCOZIAGID-LWGWVAHUSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	BA [auth E] CA [auth E] DA [auth E] GA [auth F] H [auth A] BA [auth E], CA [auth E], DA [auth E], GA [auth F], H [auth A], HA [auth F], I [auth A], IA [auth F], J [auth A], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	EA [auth E] JA [auth F] K [auth A] P [auth B] U [auth C] EA [auth E], JA [auth F], K [auth A], P [auth B], U [auth C], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]