Macromolecule Content

Total Structure Weight: 39.89 kDa
Atom Count: 3058
Residue Count: 341
Unique protein chains: 1

5NZY

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

DOI: 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

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

To Be published

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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
Find proteins for Q6PJP8 (Homo sapiens) Explore Q6PJP8 Go to UniProtKB: Q6PJP8
NIH Common Fund Data Resources
PHAROS: Q6PJP8 GTEx: ENSG00000198924
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CE3 Query on CE3 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] MOL2 format, chain C [A] MOL2 format, chain D [A]	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		Ligand Interaction
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2017-05-15
Released Date: 2017-06-14

Deposition Author(s):

Burgess-Brown, N.A.

Arrowsmith, C.H.

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.