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

Starting Model: experimental
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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] mmCIF format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF 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] mmCIF format, chain I [auth A] mmCIF 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] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF 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)

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

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)