4EFE

crystal structure of DNA ligase

PDB DOI: https://doi.org/10.2210/pdb4EFE/pdb

Classification: ligase/ligase inhibitor
Organism(s): Enterococcus faecalis
Mutation(s): No

Deposited: 2012-03-29 Released: 2013-04-03
Deposition Author(s): Wei, Y., Wang, T., Charifson, P., Xu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.254
R-Value Work: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

crystal structure of DNA ligase

Wang, T., Xu, W., Charifson, P., Wei, Y.

To be published.

Macromolecule Content

Total Structure Weight: 38.77 kDa
Atom Count: 3,029
Modelled Residue Count: 313
Deposited Residue Count: 331
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	331	Enterococcus faecalis	Mutation(s): 0 EC: 6.5.1.2
UniProt
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837V6 Go to UniProtKB: Q837V6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q837V6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMN Query on NMN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C₁₁ H₁₆ N₂ O₈ P DAYLJWODMCOQEW-TURQNECASA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
0OV Query on 0OV Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	[4-amino-2-{[(1S,2R)-2-methylcyclohexyl]oxy}-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl]acetonitrile C₁₆ H₁₉ N₅ O₂ MZUFVSMPTFUMGZ-PWSUYJOCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.254
R-Value Work: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.55	α = 90
b = 86.53	β = 101.02
c = 57.03	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2013-05-01
Changes: Other
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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Deposit Data

Help and Resources

4EFE

crystal structure of DNA ligase

crystal structure of DNA ligase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)