3C72

Engineered RabGGTase in complex with a peptidomimetic inhibitor

PDB DOI: https://doi.org/10.2210/pdb3C72/pdb

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-06 Released: 2008-07-22
Deposition Author(s): Guo, Z., Wu, Y.W., Tan, K.T., Bon, R.S., Guiu-Rozas, E., Delon, C., Nguyen, U.T., Wetzel, S., Arndt, S., Goody, R.S., Blankenfeldt, W., Alexandrov, K., Waldmann, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.256
R-Value Work: 0.189
R-Value Observed: 0.192

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Development of selective RabGGTase inhibitors and crystal structure of a RabGGTase-inhibitor complex.

Guo, Z., Wu, Y.W., Tan, K.T., Bon, R.S., Guiu-Rozas, E., Delon, C., Nguyen, T.U., Wetzel, S., Arndt, S., Goody, R.S., Blankenfeldt, W., Alexandrov, K., Waldmann, H.

(2008) Angew Chem Int Ed Engl 47: 3747-3750

PubMed: 18399557 Search on PubMed
DOI: https://doi.org/10.1002/anie.200705795
Primary Citation of Related Structures:
3C72

Organizational Affiliation

Max-Planck-Institut für molekulare Physiologie, Abt. Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 76.31 kDa
Atom Count: 5,255
Modelled Residue Count: 630
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit alpha	A	334	Rattus norvegicus	Mutation(s): 0 Gene Names: Rabggta, Ggta EC: 2.5.1.60
UniProt
Find proteins for Q08602 (Rattus norvegicus) Explore Q08602 Go to UniProtKB: Q08602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08602
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit beta	B	331	Rattus norvegicus	Mutation(s): 0 Gene Names: Rabggtb, Ggtb EC: 2.5.1.60
UniProt
Find proteins for Q08603 (Rattus norvegicus) Explore Q08603 Go to UniProtKB: Q08603
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08603
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CX1 Query on CX1 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]	N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine C₃₃ H₃₅ N₅ O₇ CPZRYRVSOCXUSE-AWCRTANDSA-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 C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
CX1	PDBBind: 3C72	IC50: 2.27e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.256
R-Value Work: 0.189
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.192	α = 90
b = 91.671	β = 90
c = 115.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description