4YU8 | pdb_00004yu8

Crystal structure of Neuroblastoma suppressor of tumorigenicity 1

• PDB DOI: https://doi.org/10.2210/pdb4YU8/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-03-18 Released: 2015-03-25 
• Deposition Author(s): Ren, J., Nettleship, J.E., Stammers, D.K., Owens, R.J., Oxford Protein Production Facility (OPPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Neuroblastoma suppressor of tumorigenicity 1

Ren, J., Nettleship, J.E., Stammers, D.K., Owens, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.42 kDa 
• Atom Count: 639 
• Modeled Residue Count: 72 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroblastoma suppressor of tumorigenicity 1	A	139	Homo sapiens	Mutation(s): 0  Gene Names: NBL1, DAN, DAND1
UniProt & NIH Common Fund Data Resources
Find proteins for P41271 (Homo sapiens) Explore P41271  Go to UniProtKB:  P41271
PHAROS:  P41271 GTEx:  ENSG00000158747
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P41271-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.069	α = 90
b = 37.069	β = 90
c = 127.856	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Ren, J., Nettleship, J.E., Stammers, D.K., Owens, R.J., Oxford Protein Production Facility (OPPF)

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary