8RIP

Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound malonate and Coenzyme A

PDB DOI: https://doi.org/10.2210/pdb8RIP/pdb

Classification: LYASE
Organism(s): Paracoccus denitrificans PD1222
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-19 Released: 2025-01-01
Deposition Author(s): Marchal, D.G., Zarzycki, J., Erb, T.J.
Funding Organization(s): Max Planck Society, European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.178 (Depositor), 0.178 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design and implementation of aerobic, ambient CO2-reduction as an entry-point for enhanced carbon fixation

Satanowski, A.G., Marchal, D.G., Perret, A., Petit, J.-L., Bouzon, M., Doering, V., Dubois, I., He, H., Smith, E.N., Pellouin, V., Petri, H.M., Rainaldi, V., Nattermann, M., Burgener, S., Paczia, N., Zarzycki, J., Heinemann, M., Bar-Even, A., Erb, T.J.

(null) Nat Commun

Macromolecule Content

Total Structure Weight: 147.92 kDa
Atom Count: 10,467
Modelled Residue Count: 1,237
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-keto-5-aminohexanoate cleavage protein	A, B, C, D	334	Paracoccus denitrificans PD1222	Mutation(s): 0 Gene Names: Pden_3578
UniProt
Find proteins for A1B802 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B802 Go to UniProtKB: A1B802
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B802
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
MLI (Subject of Investigation/LOI) Query on MLI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	G [auth A], J [auth B], L [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]