5VT3

High resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD

PDB DOI: https://doi.org/10.2210/pdb5VT3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio fluvialis
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-05-15 Released: 2017-05-31
Deposition Author(s): Chang, C., Grimshaw, S., Maltseva, N., Mulligan, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.198
R-Value Work: 0.152
R-Value Observed: 0.154

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

High resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD

Chang, C., Grimshaw, S., Maltseva, N., Mulligan, R., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 72.9 kDa
Atom Count: 5,631
Modelled Residue Count: 632
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A, B	322	Vibrio fluvialis	Mutation(s): 0 Gene Names: trxB, VFL11327_00718 EC: 1.8.1.9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B]	G [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.198
R-Value Work: 0.152
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m35vt3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.931	α = 90
b = 100.758	β = 90
c = 126.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-05-31
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary