3DZG
Crystal structure of human CD38 extracellular domain, ara-F-ribose-5'-phosphate/nicotinamide complex
- PDB DOI: https://doi.org/10.2210/pdb3DZG/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): Yes 
- Deposited: 2008-07-29 Released: 2008-11-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.211 
- R-Value Work: 0.174 
- R-Value Observed: 0.176 
wwPDB Validation   3D Report Full Report
This is version 1.5 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 |
ADP-ribosyl cyclase 1 | 262 | Homo sapiens | Mutation(s): 5  Gene Names: CD38 EC: 3.2.2.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P28907 (Homo sapiens) Explore P28907  Go to UniProtKB:  P28907 | |||||
PHAROS:  P28907 GTEx:  ENSG00000004468  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P28907 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
RF5 Query on RF5 | C [auth A], E [auth B] | 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinofuranose C5 H10 F O7 P NOTDWSJIOCLYHZ-LECHCGJUSA-N | |||
NCA Query on NCA | D [auth A], F [auth B] | NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.211 
- R-Value Work: 0.174 
- R-Value Observed: 0.176 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 41.689 | α = 106.06 |
b = 52.812 | β = 91.95 |
c = 65.381 | γ = 95.12 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2008-11-04  Deposition Author(s): Liu, Q., Kriksunov, I.A., Jiang, H., Graeff, R., Lin, H., Lee, H.C., Hao, Q.
Revision History (Full details and data files)
- Version 1.0: 2008-11-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2016-06-08
Changes: Non-polymer description - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations - Version 1.4: 2021-10-20
Changes: Database references, Structure summary - Version 1.5: 2023-08-30
Changes: Data collection, Refinement description