5JNO

Crystal structure of the BD1-NTPR complex from BEND3 and PICH

• PDB DOI: https://doi.org/10.2210/pdb5JNO/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-30 Released: 2017-09-13 
• Deposition Author(s): Pitchai, G., Mesa, P., Hickson, I.D., Montoya, G.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Crystal structure of the BD1-NTPR complex from BEND3 and PICH

Pitchai, G., Mesa, P., Hickson, I.D., Montoya, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.47 kDa 
• Atom Count: 1,283 
• Modelled Residue Count: 154 
• Deposited Residue Count: 169 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BEN domain-containing protein 3	A	112	Homo sapiens	Mutation(s): 0  Gene Names: BEND3, KIAA1553
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T5X7 (Homo sapiens) Explore Q5T5X7  Go to UniProtKB:  Q5T5X7
PHAROS:  Q5T5X7 GTEx:  ENSG00000178409

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-6-like	B	57	Homo sapiens	Mutation(s): 0  Gene Names: ERCC6L, PICH EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q2NKX8 (Homo sapiens) Explore Q2NKX8  Go to UniProtKB:  Q2NKX8
PHAROS:  Q2NKX8 GTEx:  ENSG00000186871

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.28	α = 90
b = 47.28	β = 90
c = 431.579	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHELXDE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Pitchai, G., Mesa, P., Hickson, I.D., Montoya, G.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	14cc0001

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references