8VZ4

L54G Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)

PDB DOI: https://doi.org/10.2210/pdb8VZ4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-02-09 Released: 2024-04-17
Deposition Author(s): Fried, S.D.E., Boxer, S.G.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.195
R-Value Work: 0.164
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase

Fried, S.D.E., Mukherjee, S., Mao, Y., Boxer, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 37.41 kDa
Atom Count: 3,236
Modelled Residue Count: 311
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	159	Escherichia coli	Mutation(s): 1 Gene Names: folA, tmrA, b0048, JW0047 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4 Go to UniProtKB: P0ABQ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.195
R-Value Work: 0.164
R-Value Observed: 0.165
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.493	α = 90
b = 58.592	β = 102.08
c = 70.208	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Fried, S.D.E.

Boxer, S.G.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1915727
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118044

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

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Help and Resources

8VZ4

L54G Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)

Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)