3DKJ
Crystal structure of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate
- PDB DOI: https://doi.org/10.2210/pdb3DKJ/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2008-06-25 Released: 2009-08-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.209 
- R-Value Work: 0.168 
- R-Value Observed: 0.170 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Nicotinamide phosphoribosyltransferase | 484 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P43490 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PRP Query on PRP | C [auth A], E [auth B] | 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N | |||
UNU Query on UNU | D [auth A], F [auth B] | BENZAMIDE C7 H7 N O KXDAEFPNCMNJSK-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.209 
- R-Value Work: 0.168 
- R-Value Observed: 0.170 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 61.257 | α = 90 |
b = 106.811 | β = 96.72 |
c = 83.045 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2009-08-18  Deposition Author(s): Ho, M., Burgos, E.S., Almo, S.C., Schramm, V.L.
Revision History (Full details and data files)
- Version 1.0: 2009-08-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary