Macromolecule Content

Total Structure Weight: 25.62 kDa
Atom Count: 1,574
Modelled Residue Count: 174
Deposited Residue Count: 222
Unique protein chains: 1

5UB8

Crystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II)

PDB DOI: 10.2210/pdb5UB8/pdb

Classification: PROTEIN BINDING
Organism(s): Candida albicans SC5314
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-12-20 Released: 2017-01-11
Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.226
R-Value Work: 0.185
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II)

Stogios, P.J.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Likely rab family GTP-binding protein	A	222	Candida albicans SC5314	Mutation(s): 0 Gene Names: YPT31, CaO19.10153, CaO19.2622, orf19.2622, CAALFM_CR07520CA, orf19.10153
UniProt
Find proteins for A0A1D8PTI2 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore A0A1D8PTI2 Go to UniProtKB: A0A1D8PTI2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1D8PTI2
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.226
R-Value Work: 0.185
R-Value Observed: 0.189
Space Group: C 1 2 1
Diffraction Data DOI: 10.18430/M35UB8 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.303	α = 90
b = 43.392	β = 89.05
c = 41.662	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-11

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSCN27220120026C

Revision History (Full details and data files)

Version 1.0: 2017-01-11
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-11
Changes: Author supporting evidence

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.