5NZY

Crystal structure of DNA cross-link repair protein 1A in complex with Cefotaxime

• PDB DOI: https://doi.org/10.2210/pdb5NZY/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-05-15 Released: 2017-06-14 
• Deposition Author(s): Newman, J.A., Aitkenhead, H., Kupinska, K., Burgess-Brown, N.A., Talon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.246 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Crystal structure of DNA cross-link repair protein 1A in complex with Cefotaxime

Newman, J.A., Aitkenhead, H., Kupinska, K., Burgess-Brown, N.A., Talon, 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 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.89 kDa 
• Atom Count: 3,058 
• 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
CE3	C [auth A], D [auth A]	(6R,7R)-3-(acetyloxymethyl)-7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-8-oxo-5-thia-1-azabicy clo[4.2.0]oct-2-ene-2-carboxylic acid C16 H17 N5 O7 S2 GPRBEKHLDVQUJE-QSWIMTSFSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.246 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.122	α = 90
b = 55.83	β = 90
c = 112.743	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Newman, J.A., Aitkenhead, H., Kupinska, K., Burgess-Brown, N.A., Talon, R., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary