8PMK

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


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phthaloyl-CoA decarboxylase
A, B, C, D, E
A, B, C, D, E, F
527Thauera chlorobenzoicaMutation(s): 0 
Gene Names: Tchl_3080
UniProt
Find proteins for A0A193DUB4 (Thauera chlorobenzoica)
Explore A0A193DUB4 
Go to UniProtKB:  A0A193DUB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A193DUB4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYN (Subject of Investigation/LOI)
Query on BYN

Download Ideal Coordinates CCD File 
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
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
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
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release