2AMT

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor

PDB DOI: https://doi.org/10.2210/pdb2AMT/pdb

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

Deposited: 2005-08-10 Released: 2006-02-28
Deposition Author(s): Ramsden, N.L., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.280
R-Value Work: 0.243
R-Value Observed: 0.245

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: 105.94 kDa
Atom Count: 7,495
Modelled Residue Count: 936
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

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(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, B, C, D, E A, B, C, D, E, F	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
1AA Query on 1AA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E]	H [auth A] L [auth C] M [auth C] O [auth D] R [auth E] H [auth A], L [auth C], M [auth C], O [auth D], R [auth E], S [auth E]	5'-O-[({[(2-{[(2-AMINOPHENYL)CARBONYL]OXY}ETHYL)OXY]PHOSPHINATO}OXY)PHOSPHINATO]CYTIDINE C₁₈ H₂₄ N₄ O₁₃ P₂ PGXVRIOOHRVKLC-DTZQCDIJSA-N		Interactions Focus chain H [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E]
GPP Query on GPP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth D]	I [auth A], P [auth D]	GERANYL DIPHOSPHATE C₁₀ H₂₀ O₇ P₂ GVVPGTZRZFNKDS-JXMROGBWSA-N		Interactions Focus chain I [auth A] Focus chain P [auth D] Interactions & Density Focus chain I [auth A] Focus chain P [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain T [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F]	G [auth A] J [auth B] K [auth C] N [auth D] Q [auth E] G [auth A], J [auth B], K [auth C], N [auth D], Q [auth E], T [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain T [auth F]

Binding Affinity Annotations
ID	Source	Binding Affinity
1AA	PDBBind: 2AMT	Kd: 3.60e+4 (nM) from 1 assay(s)
1AA	Binding MOAD: 2AMT	Kd: 3.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.280
R-Value Work: 0.243
R-Value Observed: 0.245
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.033	α = 90
b = 115.269	β = 90.18
c = 87.609	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-02-28

Deposition Author(s):

Ramsden, N.L.

Hunter, W.N.

Revision History (Full details and data files)

Version 1.0: 2006-02-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

2AMT

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)