5LX3 | pdb_00005lx3

CRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782.

PDB DOI: https://doi.org/10.2210/pdb5LX3/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-20 Released: 2017-10-25
Deposition Author(s): Bertrand, T., Marquette, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.211 (Depositor), 0.198 (DCC)
R-Value Work:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782.

Bertrand, T., Marquette, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 112.52 kDa
Atom Count: 8,457
Modeled Residue Count: 926
Deposited Residue Count: 986
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	493	Homo sapiens	Mutation(s): 0 Gene Names: NAMPT, PBEF, PBEF1 EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens) Explore P43490 Go to UniProtKB: P43490
PHAROS: P43490 GTEx: ENSG00000105835
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7A1 Query on 7A1 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	6-[4-[(6-azanylpyridin-3-yl)methylcarbamoylamino]-3-fluoranyl-phenyl]-2-(ethylamino)-~{N}-(2-piperidin-1-ylethyl)pyridine-3-carboxamide C₂₈ H₃₅ F N₈ O₂ JXVZQJNZEWWAKF-UHFFFAOYSA-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: 2.10 Å
R-Value Free: 0.211 (Depositor), 0.198 (DCC)
R-Value Work: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.51	α = 90
b = 107.13	β = 96.69
c = 83.59	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XDS	data reduction
Aimless	data scaling
BUSTER-TNT	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Marquette, J.P.

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.