6TB6 | pdb_00006tb6

Crystal structure of formate dehydrogenase FDH2 D222S/Q223R enzyme from Granulicella mallensis MP5ACTX8 in complex with NADP and azide.

PDB DOI: https://doi.org/10.2210/pdb6TB6/pdb

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

Deposited: 2019-11-01 Released: 2020-08-05
Deposition Author(s): Robescu, M.S., Rubini, R., Filippini, F., Bergantino, B., Cendron, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.206 (Depositor), 0.213 (DCC)
R-Value Work:
0.154 (Depositor), 0.172 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

From the Amelioration of a NADP+-dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice

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

(2020) ChemCatChem

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

Macromolecule Content

Total Structure Weight: 43.49 kDa
Atom Count: 3,367
Modeled Residue Count: 374
Deposited Residue Count: 386
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 B]	386	Granulicella mallensis	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]
AZI (Subject of Investigation/LOI) Query on AZI Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]