4RY3 | pdb_00004ry3

Crystal structure of human Fanconi-associated nuclease 1

PDB DOI: https://doi.org/10.2210/pdb4RY3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2014-12-13 Released: 2015-01-28
Deposition Author(s): Yan, P.X., Huo, Y.G., Jiang, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.243 (Depositor), 0.247 (DCC)
R-Value Work:
0.208 (Depositor), 0.213 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4RY3

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

Literature

Crystal structure of human Fanconi-associated nuclease 1.

Yan, P.X., Huo, Y.G., Jiang, T.

(2015) Protein Cell 6: 225-228

PubMed: 25547363 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s13238-014-0128-y
Primary Citation Related Structures:
4RY3

Organizational Affiliation

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 74.05 kDa
Atom Count: 4,775
Modeled Residue Count: 593
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fanconi-associated nuclease 1	A	648	Homo sapiens	Mutation(s): 0 Gene Names: FAN1, KIAA1018, MTMR15 EC: 3.1.21 (PDB Primary Data), 3.1.4.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2M0 (Homo sapiens) Explore Q9Y2M0 Go to UniProtKB: Q9Y2M0
PHAROS: Q9Y2M0 GTEx: ENSG00000198690
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2M0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT 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]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-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: 2.80 Å
R-Value Free: 0.243 (Depositor), 0.247 (DCC)
R-Value Work: 0.208 (Depositor), 0.213 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.082	α = 90
b = 161.082	β = 90
c = 161.082	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2022-08-24
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

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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.