5NZX | pdb_00005nzx

Crystal structure of DNA cross-link repair protein 1A in complex with Ceftriaxone (alternative site)

• PDB DOI: https://doi.org/10.2210/pdb5NZX/pdb

• Classification: HYDROLASE
• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DNA cross-link repair protein 1A in complex with Ceftriaxone (alternative site)

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: 39.54 kDa 
• Atom Count: 2,883 
• Modelled Residue Count: 336 
• 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
9F2	C [auth A]	Ceftriaxone C18 H18 N8 O7 S3 VAAUVRVFOQPIGI-TYHRLYECSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.45	α = 90
b = 56.55	β = 90
c = 113.52	γ = 90

Software Package:

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

Structure Validation

Entry History 

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.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary