9CSN | pdb_00009csn

Crystal structure of human ribonuclease 7 (RNase 7) in complex with 5'-adenosine monophosphate (5'-AMP)

PDB DOI: https://doi.org/10.2210/pdb9CSN/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: 2.07 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human ribonuclease 7 (RNase 7) in complex with 5'-adenosine monophosphate (5'-AMP)

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

To be published.

Macromolecule Content

Total Structure Weight: 30.54 kDa
Atom Count: 2,199
Modeled Residue Count: 256
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 7	A, B	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	H [auth A], K [auth A], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
BO3 Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B]	C [auth A] D [auth A] E [auth A] I [auth A] J [auth A] C [auth A], D [auth A], E [auth A], I [auth A], J [auth A], O [auth B]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.262 (Depositor), 0.263 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.11	α = 90
b = 48.17	β = 97.28
c = 62.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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