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), 0.207 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 39.54 kDa
Atom Count: 2,883
Modeled Residue Count: 336
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
9F2 Query on 9F2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Ceftriaxone C₁₈ H₁₈ N₈ O₇ S₃ VAAUVRVFOQPIGI-TYHRLYECSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [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: 1.47 Å
R-Value Free: 0.207 (Depositor), 0.207 (DCC)
R-Value Work: 0.168 (Depositor), 0.168 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

Revision History (Full details and data files)

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