7WP3 | pdb_00007wp3

Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution

PDB DOI: https://doi.org/10.2210/pdb7WP3/pdb
Entry: 7WP3 supersedes: 5B7O

Classification: DNA BINDING PROTEIN
Organism(s): Leishmania donovani
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-22 Released: 2022-06-15
Deposition Author(s): Ahmad, M.I., Yadav, S.P., Singh, P.K., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.257 (Depositor), 0.253 (DCC)
R-Value Work:
0.211 (Depositor), 0.214 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution

Ahmad, M.I., Yadav, S.P., Singh, P.K., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 191.9 kDa
Atom Count: 11,628
Modeled Residue Count: 1,488
Deposited Residue Count: 1,734
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A, B, C, D, E A, B, C, D, E, F	289	Leishmania donovani	Mutation(s): 0 Gene Names: PCNA
UniProt
Find proteins for B5TV91 (Leishmania donovani) Explore B5TV91 Go to UniProtKB: B5TV91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5TV91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNT (Subject of Investigation/LOI) Query on PNT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth C]	G [auth A], H [auth C]	1,5-BIS(4-AMIDINOPHENOXY)PENTANE C₁₉ H₂₄ N₄ O₂ XDRYMKDFEDOLFX-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.257 (Depositor), 0.253 (DCC)
R-Value Work: 0.211 (Depositor), 0.214 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.024	α = 90
b = 150.664	β = 90
c = 170.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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: 2022-06-15

Deposition Author(s):

This entry supersedes: 5B7O

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	DBT/2020/July/86

Revision History (Full details and data files)

Version 1.0: 2022-06-15
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.