8CEW

Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1

• PDB DOI: https://doi.org/10.2210/pdb8CEW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-02-02 Released: 2024-02-21 
• Deposition Author(s): Newman, J.A., Yosaatmadja, Y., Baddock, H.T., Bielinski, M., von Delft, F., Bountra, C., McHugh, P.J., Schofield, C.J., Gileadi, O.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.224 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1

Newman, J.A., Yosaatmadja, Y., Baddock, H.T., Bielinski, M., von Delft, F., Bountra, C., McHugh, P.J., Schofield, C.J., Gileadi, O.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.83 kDa 
• Atom Count: 3,027 
• Modelled Residue Count: 341 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA cross-link repair 1A protein	A	345	Homo sapiens	Mutation(s): 0  Gene Names: DCLRE1A, KIAA0086, SNM1, SNM1A EC: 3.5.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PJP8 (Homo sapiens) Explore Q6PJP8  Go to UniProtKB:  Q6PJP8
PHAROS:  Q6PJP8 GTEx:  ENSG00000198924

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UFI (Subject of Investigation/LOI)	E [auth A], F [auth A]	6-methoxy-2-oxidanyl-benzo[de]isoquinoline-1,3-dione C13 H9 N O4 JNZJPCRGQNFNFC-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.224 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.59	α = 90
b = 56.5	β = 90
c = 113.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Newman, J.A., Yosaatmadja, Y., Baddock, H.T., Bielinski, M., von Delft, F., Bountra, C., McHugh, P.J., Schofield, C.J., Gileadi, O.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release