8P02 | pdb_00008p02

Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb8P02/pdb
EM Map EMD-17324: EMDB EMDataResource

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

Deposited: 2023-05-09 Released: 2024-06-05
Deposition Author(s): Kayastha, K., Ermler, U.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA

Kayastha, K., Ermler, U.

To be published.

Macromolecule Content

Total Structure Weight: 355.72 kDa
Atom Count: 24,929
Modeled Residue Count: 3,084
Deposited Residue Count: 3,084
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phthaloyl-CoA decarboxylase (Pcd)	A, B, C, D, E A, B, C, D, E, F	514	Thauera chlorobenzoica	Mutation(s): 0
UniProt
Find proteins for A0A193DUB4 (Thauera chlorobenzoica) Explore A0A193DUB4 Go to UniProtKB: A0A193DUB4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A193DUB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BYC (Subject of Investigation/LOI) Query on BYC Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain KA [auth F] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	EA [auth E] G [auth A] KA [auth F] M [auth B] S [auth C] EA [auth E], G [auth A], KA [auth F], M [auth B], S [auth C], Y [auth D]	benzoyl coenzyme A C₂₈ H₄₀ N₇ O₁₇ P₃ S VEVJTUNLALKRNO-TYHXJLICSA-N		Interactions Focus chain EA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
BYN (Subject of Investigation/LOI) Query on BYN Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain H [auth A] SDF format, chain LA [auth F] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	FA [auth E] H [auth A] LA [auth F] N [auth B] T [auth C] FA [auth E], H [auth A], LA [auth F], N [auth B], T [auth C], Z [auth D]	hydroxylated prenyl-FMN C₂₂ H₃₁ N₄ O₁₀ P BDNVCRCOZIAGID-LWGWVAHUSA-N		Interactions Focus chain FA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	AA [auth D] BA [auth D] GA [auth E] HA [auth E] I [auth A] AA [auth D], BA [auth D], GA [auth E], HA [auth E], I [auth A], J [auth A], MA [auth F], NA [auth F], O [auth B], P [auth B], U [auth C], V [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain IA [auth E] SDF format, chain OA [auth F] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain K [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain K [auth A]	CA [auth D] IA [auth E] K [auth A] OA [auth F] Q [auth B] CA [auth D], IA [auth E], K [auth A], OA [auth F], Q [auth B], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain IA [auth E] Focus chain K [auth A] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain IA [auth E] Focus chain K [auth A] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain W [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain PA [auth F] SDF format, chain R [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C]	DA [auth D] JA [auth E] L [auth A] PA [auth F] R [auth B] DA [auth D], JA [auth E], L [auth A], PA [auth F], R [auth B], X [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain JA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain JA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain R [auth B] Focus chain X [auth C]