5CYP | pdb_00005cyp

GTPase domain of Septin 9 in complex with GTP-gamma-S

PDB DOI: https://doi.org/10.2210/pdb5CYP/pdb

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

Deposited: 2015-07-30 Released: 2016-08-03
Deposition Author(s): Matos, S.S., Leonardo, D.A., Pereira, H.M., Horjales, E., Araujo, A.P.U., Garratt, R.C.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.297 (Depositor), 0.300 (DCC)
R-Value Work:
0.252 (Depositor), 0.250 (DCC)
R-Value Observed:
0.254 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface

Castro, D.K.S.V., da Silva, S.M.O., Pereira, H.M., Macedo, J.N.A., Leonardo, D.A., Valadares, N.F., Kumagai, P.S., Brandao-Neto, J., Araujo, A.P.U., Garratt, R.C.

(2020) IUCrJ

DOI: https://doi.org/10.1107/S2052252520002973

Macromolecule Content

Total Structure Weight: 130.16 kDa
Atom Count: 7,249
Modeled Residue Count: 940
Deposited Residue Count: 1,096
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Septin-9	A, B, C, D	274	Homo sapiens	Mutation(s): 0 Gene Names: SEPT9, KIAA0991, MSF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHD8 (Homo sapiens) Explore Q9UHD8 Go to UniProtKB: Q9UHD8
PHAROS: Q9UHD8 GTEx: ENSG00000184640
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSP Query on GSP Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ S XOFLBQFBSOEHOG-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.297 (Depositor), 0.300 (DCC)
R-Value Work: 0.252 (Depositor), 0.250 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.587	α = 90
b = 79.156	β = 100.38
c = 108.217	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-08-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/15546-1

Revision History (Full details and data files)

Version 1.0: 2016-08-03
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Refinement description
Version 1.2: 2017-11-01
Changes: Author supporting evidence
Version 1.3: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.4: 2020-01-01
Changes: Author supporting evidence
Version 1.5: 2020-04-22
Changes: Database references
Version 1.6: 2020-05-13
Changes: Database references
Version 1.7: 2024-03-06
Changes: Data collection, Database references, Derived calculations