9R7F | pdb_00009r7f

De novo designed enzyme for the Morita-Baylis-Hillman reaction (MBH48)

PDB DOI: https://doi.org/10.2210/pdb9R7F/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-14 Released: 2025-12-10
Deposition Author(s): Tripp, A., Fischer, C., Moser, M., Oberdorfer, G.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.252 (Depositor), 0.249 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Computational enzyme design by catalytic motif scaffolding

Braun, M., Tripp, A., Chakatok, M., Kaltenbrunner, S., Fischer, C., Stoll, D., Bijelic, A., Elaily, W., Totaro, M.G., Moser, M., Hoch, S.Y., Lechner, H., Rossi, F., Aleotti, M., Hall, M., Oberdorfer, G.

(2025) Nature

DOI: https://doi.org/10.1038/s41586-025-09747-9

Macromolecule Content

Total Structure Weight: 24.34 kDa
Atom Count: 1,649
Modeled Residue Count: 202
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MBH48	A	221	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A]	J [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain L [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A]