2GZL

Structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with a CDP derived fluorescent inhibitor

PDB DOI: https://doi.org/10.2210/pdb2GZL/pdb
Entry: 2GZL supersedes: 2AO4

Classification: LYASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-05-11 Released: 2006-11-14
Deposition Author(s): Crane, C.M., Kaiser, J., Ramsden, N.L., Lauw, S., Rohdich, F., Wolfgang, E., Hunter, W.N., Bacher, A., Diederich, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.207
R-Value Observed: 0.209

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

Fluorescent Inhibitors for Ispf, an Enzyme in the Non-Mevalonate Pathway for Isoprenoid Biosynthesis and a Potential Target for Antimalarial Therapy.

Crane, C.M., Kaiser, J., Ramsden, N.L., Lauw, S., Rohdich, F., Eisenreich, W., Hunter, W.N., Bacher, A., Diederich, F.

(2006) Angew Chem Int Ed Engl 45: 1069-1074

PubMed: 16392111 Search on PubMed
DOI: https://doi.org/10.1002/anie.200503003
Primary Citation of Related Structures:
2AMT, 2GZL

Organizational Affiliation

Laboratorium für Organische Chemie, ETH Hönggerberg, HCI, 8093 Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 17.99 kDa
Atom Count: 1,295
Modelled Residue Count: 159
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A	159	Escherichia coli	Mutation(s): 0 Gene Names: ispF, mecS EC: 4.6.1.12
UniProt
Find proteins for P62617 (Escherichia coli (strain K12)) Explore P62617 Go to UniProtKB: P62617
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62617
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2AA Query on 2AA 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]	5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT C₂₃ H₃₁ N₅ O₁₃ P₂ S OXPWLEWKRGQJQO-BRKWEVRTSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GPP Query on GPP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GERANYL DIPHOSPHATE C₁₀ H₂₀ O₇ P₂ GVVPGTZRZFNKDS-JXMROGBWSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
2AA	PDBBind: 2GZL	Kd: 1.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.207
R-Value Observed: 0.209
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.098	α = 90
b = 145.098	β = 90
c = 145.098	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-11-14

Deposition Author(s):

This entry supersedes: 2AO4

Revision History (Full details and data files)

Version 1.0: 2006-11-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description