1ZBH | pdb_00001zbh

3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease

PDB DOI: https://doi.org/10.2210/pdb1ZBH/pdb
NAKB: 1ZBH

Classification: HYDROLASE/RNA
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-04-08 Released: 2006-09-26
Deposition Author(s): Cheng, Y., Patel, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.260 (Depositor), 0.283 (DCC)
R-Value Work:
0.209 (Depositor), 0.264 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural basis for 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease, a human nuclease that also targets siRNA

Cheng, Y., Patel, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 152.91 kDa
Atom Count: 9,138
Modeled Residue Count: 1,060
Deposited Residue Count: 1,236
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3'-5' exonuclease ERI1	C [auth A], D [auth B], E [auth C], F [auth D]	299	Homo sapiens	Mutation(s): 2 Gene Names: ERI1, 3'EXO EC: 3.1 (PDB Primary Data), 3.1.13.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV48 (Homo sapiens) Explore Q8IV48 Go to UniProtKB: Q8IV48
PHAROS: Q8IV48 GTEx: ENSG00000104626
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IV48
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
5'-R(CPCPGPGPCPUPCPUPUPUPUPCPAPGPAPGPCPCPGPG)-3'	A [auth F], B [auth E]	20	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	I [auth A], L [auth B], O [auth C], R [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] J [auth B] K [auth B] M [auth C] G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D]