4UCU

Fragment bound to H.influenza NAD dependent DNA ligase

PDB DOI: https://doi.org/10.2210/pdb4UCU/pdb

Deposited: 2014-12-04 Released: 2015-10-14
Deposition Author(s): Hale, M., Brassington, C., Carcanague, D., Embrey, K., Eyermann, C.J., Giacobbe, R.A., Gingipali, L., Gowravaram, M., Harang, J., Howard, T., Ioannidis, G., Jahic, H., Kutschke, A., Laganas, V.A., Loch, J., Miller, M.D., Murphy-Benenato, K.E., Oguto, H., Otterbein, L., Patel, S.J., Shapiro, A.B., Boriack-Sjodin, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.260
R-Value Work: 0.224
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

From Fragments to Leads: Novel Bacterial Nad+-Dependent DNA Ligase Inhibitors

Hale, M., Brassington, C., Carcanague, D., Embrey, K., Eyermann, C.J., Giacobbe, R.A., Gingipali, L., Gowravaram, M., Harang, J., Howard, T., Ioannidis, G., Jahic, H., Kutschke, A., Laganas, V.A., Loch, J., Miller, M.D., Murphy-Benenato, K.E., Oguto, H., Otterbein, L., Patel, S.J., Shapiro, A.B., Boriack-Sjodin, P.A.

(2015) Tetrahedron Lett 56: 3108

DOI: https://doi.org/10.1016/J.TETLET.2014.12.067

Macromolecule Content

Total Structure Weight: 36.96 kDa
Atom Count: 2,702
Modelled Residue Count: 318
Deposited Residue Count: 324
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	324	Haemophilus influenzae	Mutation(s): 0 EC: 6.5.1.2
UniProt
Find proteins for P43813 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43813 Go to UniProtKB: P43813
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43813
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IWH Query on IWH Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide C₁₅ H₁₆ N₂ O₂ TUJVPUNUHQIBSM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
8HC Query on 8HC 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]	8-hydroxyquinoline-2-carboxylic acid C₁₀ H₇ N O₃ UHBIKXOBLZWFKM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.260
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.147	α = 90
b = 139.147	β = 90
c = 56.124	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Murphy-Benenato, K.E.

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-06-28
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

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4UCU

Fragment bound to H.influenza NAD dependent DNA ligase

From Fragments to Leads: Novel Bacterial Nad+-Dependent DNA Ligase Inhibitors

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)