5QSP | pdb_00005qsp

PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434929

PDB DOI: https://doi.org/10.2210/pdb5QSP/pdb
Deposition Group: G_1002083 (changed state) | Explore G_1002083

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-25 Released: 2019-08-21
Deposition Author(s): Newman, J.A., Katis, V.L., Gavard, A.E., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.263 (Depositor)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

PanDDA analysis group deposition

Newman, J.A., Katis, V.L., Gavard, A.E., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 105.75 kDa
Atom Count: 7,079
Modeled Residue Count: 860
Deposited Residue Count: 918
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cohesin subunit SA-1	A, B	459	Homo sapiens	Mutation(s): 0 Gene Names: STAG1, SA1, SCC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVM7 (Homo sapiens) Explore Q8WVM7 Go to UniProtKB: Q8WVM7
PHAROS: Q8WVM7 GTEx: ENSG00000118007
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WVM7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LVV (Subject of Investigation/LOI) Query on LVV Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-[(4-methylphenyl)methyl]-1,4-thiazinane 1,1-dioxide C₁₂ H₁₇ N O₂ S PBEMXBVPRZGFNM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.263 (Depositor)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.754	α = 90
b = 166.322	β = 90
c = 46.775	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2026-02-18
Changes: Refinement description, Structure summary

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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.