5Q1K | pdb_00005q1k

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000074a

• PDB DOI: https://doi.org/10.2210/pdb5Q1K/pdb
• Deposition Group: G_1002034 | Explore  G_1002034  

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


• Deposited: 2017-05-15 Released: 2018-08-08 
• Deposition Author(s): Newman, J.A., Aitkenhead, H., Lee, S.Y., Kupinska, K., Burgess-Brown, N., Tallon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Newman, J.A., Aitkenhead, H., Lee, S.Y., Kupinska, K., Burgess-Brown, N., Tallon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.32 kDa 
• Atom Count: 3,143 
• Modeled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AW7	D [auth A]	2-[4-(1~{H}-pyrazol-3-yl)phenoxy]pyrimidine C13 H10 N4 O DUEUESIXAVJTRZ-UHFFFAOYSA-N
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.05	α = 90
b = 57.22	β = 90
c = 115.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Newman, J.A., Aitkenhead, H., Lee, S.Y., Kupinska, K., Burgess-Brown, N., Tallon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-11-20
  Changes: Structure summary
• Version 1.3: 2026-02-18
  Changes: Refinement description