9CSM | pdb_00009csm

Crystal structure of human ribonuclease 7 (RNase 7, HsR7)

PDB DOI: https://doi.org/10.2210/pdb9CSM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-24 Released: 2025-07-30
Deposition Author(s): Tran, T.T.Q., Pham, N.T.H., Calmettes, C., Doucet, N.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Fonds de Recherche du Quebec - Sante (FRQS), Canada Foundation for Innovation, Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human ribonuclease 7 (RNase 7, HsR7)

Tran, T.T.Q., Pham, N.T.H., Calmettes, C., Doucet, N.

To be published.

Macromolecule Content

Total Structure Weight: 16.22 kDa
Atom Count: 1,213
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 7	A	129	Homo sapiens	Mutation(s): 0 Gene Names: RNASE7, UNQ2516/PRO6006 EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1E1 (Homo sapiens) Explore Q9H1E1 Go to UniProtKB: Q9H1E1
PHAROS: Q9H1E1 GTEx: ENSG00000165799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H1E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain Q [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Q [auth A]	Q [auth A], X [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain X [auth A] Interactions & Density Focus chain Q [auth A] Focus chain X [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain S [auth A] MOL2 format, chain V [auth A] MOL2 format, chain S [auth A] mmCIF format, chain V [auth A] mmCIF format, chain S [auth A]	S [auth A], V [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain V [auth A] Interactions & Density Focus chain S [auth A] Focus chain V [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], O [auth A], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain R [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A]	R [auth A], T [auth A], U [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.221	α = 90
b = 62.25	β = 99.2
c = 38.276	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2022-04368
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2017-06091
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	CREATE APRENTICE
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	281993
Canada Foundation for Innovation	Canada	MSI - GlycoNet Integrated Services
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)	Canada	PROTEO