7TNV

Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117S Mutant

PDB DOI: https://doi.org/10.2210/pdb7TNV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-01-21 Released: 2023-04-12
Deposition Author(s): Zheng, A., Thibodeau, P.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (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

Structure Of wild-type Human NADH-Cytochrome B5 Reductase and mutants

Zheng, A., Thibodeau, P.H.

To be published.

Macromolecule Content

Total Structure Weight: 31.92 kDa
Atom Count: 2,481
Modelled Residue Count: 270
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-cytochrome b5 reductase 3 soluble form	A	274	Homo sapiens	Mutation(s): 1 Gene Names: CYB5R3, DIA1 EC: 1.6.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00387 (Homo sapiens) Explore P00387 Go to UniProtKB: P00387
PHAROS: P00387 GTEx: ENSG00000100243
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00387
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD 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-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.53	α = 90
b = 65.53	β = 90
c = 71.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-12

Deposition Author(s):

Thibodeau, P.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM122091

Revision History (Full details and data files)

Version 1.0: 2023-04-12
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.