4YDE | pdb_00004yde

CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb4YDE/pdb

Classification: TRANSFERASE
Organism(s): Candida albicans SC5314
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-02-22 Released: 2016-07-06
Deposition Author(s): Kumar, S., Mabanglo, M.F., Hast, M.A., Shi, Y., Beese, L.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.195 (Depositor), 0.202 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE

Kumar, S., Mabanglo, M.F., Hast, M.A., Shi, Y., Beese, L.S.

To be published.

Macromolecule Content

Total Structure Weight: 106.51 kDa
Atom Count: 6,060
Modeled Residue Count: 714
Deposited Residue Count: 916
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	A	329	Candida albicans SC5314	Mutation(s): 0 Gene Names: RAM2, CaO19.12280, CaO19.4817

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 Subunit beta	B	587	Candida albicans SC5314	Mutation(s): 0 Gene Names: RAM1, CaO19.12513

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4C7 Query on 4C7 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	(3R,7S)-3,7,11-trimethyldodecyl trihydrogen diphosphate C₁₅ H₃₄ O₇ P₂ QLJFEPYMTKDKMH-LSDHHAIUSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.195 (Depositor), 0.202 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.874	α = 90
b = 98.874	β = 90
c = 188.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2022-03-30
Changes: Author supporting evidence, Database references
Version 1.3: 2023-09-27
Changes: Data collection, Refinement description