8C8B

Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 48).

• PDB DOI: https://doi.org/10.2210/pdb8C8B/pdb

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


• Deposited: 2023-01-19 Released: 2024-01-31 
• Deposition Author(s): Yosaatmadja, Y., Newman, J.A., 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: 1.46 Å
• R-Value Free: 0.217 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 21).

Yosaatmadja, Y., Newman, J.A., 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: 39.37 kDa 
• Atom Count: 3,006 
• Modelled Residue Count: 341 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA cross-link repair 1A protein	A	343	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U1L (Subject of Investigation/LOI)	B [auth A]	4-[[(2~{S})-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-~{N}-prop-2-enyl-quinazoline-2-carboxamide C15 H17 N5 O3 ISWZNEONBBEJIZ-VIFPVBQESA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.217 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.69	α = 90
b = 57.25	β = 90
c = 113.52	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Yosaatmadja, Y., Newman, J.A., 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: 2024-01-31
  Type: Initial release