8BXX | pdb_00008bxx

Crystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in complex with NAD and azide.

PDB DOI: https://doi.org/10.2210/pdb8BXX/pdb
Entry: 8BXX supersedes: 6T8J

Classification: OXIDOREDUCTASE
Organism(s): Granulicella mallensis MP5ACTX8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-10 Released: 2023-01-18
Deposition Author(s): Robescu, M.S., Rubini, R., Filippini, F., Bergantino, B., Cendron, L.
Funding Organization(s): Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.234 (Depositor), 0.228 (DCC)
R-Value Work:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6T8J

Literature

From the amelioration of a NADP+-dependent formate dehydrogenase to the discovery of a new enzyme: round trip from theory to practice

Rubini, R., Robescu, M.S., Tavanti, M., Beneventi, E., Lonigro, C., Niero, M., Zito, F., Filippini, F., Cendron, L., Bergantino, E.

(2020) ChemCatChem

DOI: https://doi.org/10.1002/cctc.201902089

Macromolecule Content

Total Structure Weight: 173.43 kDa
Atom Count: 12,689
Modeled Residue Count: 1,480
Deposited Residue Count: 1,544
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A [auth AA], B [auth BB], C [auth CC], D [auth DD]	386	Granulicella mallensis MP5ACTX8	Mutation(s): 0 Gene Names: AciX8_0868 EC: 1.17.1.9
UniProt
Find proteins for G8NTI5 (Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8)) Explore G8NTI5 Go to UniProtKB: G8NTI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8NTI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth AA] SDF format, chain H [auth BB] SDF format, chain K [auth CC] SDF format, chain N [auth DD] MOL2 format, chain E [auth AA] MOL2 format, chain H [auth BB] MOL2 format, chain K [auth CC] MOL2 format, chain N [auth DD] mmCIF format, chain E [auth AA] mmCIF format, chain H [auth BB] mmCIF format, chain K [auth CC] mmCIF format, chain N [auth DD]	E [auth AA], H [auth BB], K [auth CC], N [auth DD]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth AA] Focus chain H [auth BB] Focus chain K [auth CC] Focus chain N [auth DD] Interactions & Density Focus chain E [auth AA] Focus chain H [auth BB] Focus chain K [auth CC] Focus chain N [auth DD]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth AA] SDF format, chain J [auth BB] SDF format, chain M [auth CC] SDF format, chain P [auth DD] MOL2 format, chain G [auth AA] MOL2 format, chain J [auth BB] MOL2 format, chain M [auth CC] MOL2 format, chain P [auth DD] mmCIF format, chain G [auth AA] mmCIF format, chain J [auth BB] mmCIF format, chain M [auth CC] mmCIF format, chain P [auth DD]	G [auth AA], J [auth BB], M [auth CC], P [auth DD]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth AA] Focus chain J [auth BB] Focus chain M [auth CC] Focus chain P [auth DD] Interactions & Density Focus chain G [auth AA] Focus chain J [auth BB] Focus chain M [auth CC] Focus chain P [auth DD]
AZI (Subject of Investigation/LOI) Query on AZI Download:Ideal Coordinates CCD File SDF format, chain F [auth AA] SDF format, chain I [auth BB] SDF format, chain L [auth CC] SDF format, chain O [auth DD] MOL2 format, chain F [auth AA] MOL2 format, chain I [auth BB] MOL2 format, chain L [auth CC] MOL2 format, chain O [auth DD] mmCIF format, chain F [auth AA] mmCIF format, chain I [auth BB] mmCIF format, chain L [auth CC] mmCIF format, chain O [auth DD]	F [auth AA], I [auth BB], L [auth CC], O [auth DD]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain F [auth AA] Focus chain I [auth BB] Focus chain L [auth CC] Focus chain O [auth DD] Interactions & Density Focus chain F [auth AA] Focus chain I [auth BB] Focus chain L [auth CC] Focus chain O [auth DD]