5NZY | pdb_00005nzy

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.206 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 39.89 kDa
Atom Count: 3,058
Modeled Residue Count: 341
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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| 3D 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 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6PJP8
Sequence Annotations 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 D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.246 (Depositor), 0.247 (DCC)
R-Value Work: 0.206 (Depositor), 0.208 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

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