5LNI | pdb_00005lni

XenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin

PDB DOI: https://doi.org/10.2210/pdb5LNI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-08-04 Released: 2017-08-16
Deposition Author(s): Werther, T., Dobbek, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.141 (Depositor), 0.137 (DCC)
R-Value Work:
0.118 (Depositor), 0.116 (DCC)
R-Value Observed:
0.118 (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

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

Werther, T., Wahlefeld, S., Salewski, J., Kuhlmann, U., Zebger, I., Hildebrandt, P., Dobbek, H.

(2017) Nat Commun 8: 16084

DOI: https://doi.org/10.1038/ncomms16084

Macromolecule Content

Total Structure Weight: 40.55 kDa
Atom Count: 3,591
Modeled Residue Count: 359
Deposited Residue Count: 359
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:flavin oxidoreductase	A	359	Pseudomonas putida	Mutation(s): 1 Gene Names: O999_23785
UniProt
Find proteins for A0A1X0ZT96 (Pseudomonas putida) Explore A0A1X0ZT96 Go to UniProtKB: A0A1X0ZT96
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1X0ZT96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
07L Query on 07L Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	7-hydroxy-2H-chromen-2-one C₉ H₆ O₃ ORHBXUUXSCNDEV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]