4X3G | pdb_00004x3g

Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide

PDB DOI: https://doi.org/10.2210/pdb4X3G/pdb

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

Deposited: 2014-11-28 Released: 2014-12-31
Deposition Author(s): Walker, J.R., Dong, A., Zhang, Q., Huang, X., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.251 (Depositor), 0.274 (DCC)
R-Value Work:
0.222 (Depositor), 0.234 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide

Walker, J.R., Dong, A., Zhang, Q., Huang, X., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 46.59 kDa
Atom Count: 3,173
Modeled Residue Count: 399
Deposited Residue Count: 414
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SIAH1	A, B	193	Homo sapiens	Mutation(s): 0 Gene Names: SIAH1, HUMSIAH EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUQ4 (Homo sapiens) Explore Q8IUQ4 Go to UniProtKB: Q8IUQ4
PHAROS: Q8IUQ4 GTEx: ENSG00000196470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IUQ4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 19	C, D	14	Homo sapiens	Mutation(s): 0 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94966 (Homo sapiens) Explore O94966 Go to UniProtKB: O94966
PHAROS: O94966 GTEx: ENSG00000172046
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O94966
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.251 (Depositor), 0.274 (DCC)
R-Value Work: 0.222 (Depositor), 0.234 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.343	α = 90
b = 88.092	β = 103.24
c = 59.59	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-12-31
Type: Initial release
Version 1.1: 2016-04-27
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Database references, Derived calculations
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description