4Z7M | pdb_00004z7m

Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity

PDB DOI: https://doi.org/10.2210/pdb4Z7M/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-04-07 Released: 2016-04-13
Deposition Author(s): Rose, J.A., Lahiri, S.D., McKinney, D.C., Albert, R., Morningstar, M., Shapiro, A.B., Fisher, S.F., Fleming, P.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.305 (Depositor), 0.312 (DCC)
R-Value Work:
0.251 (Depositor), 0.259 (DCC)
R-Value Observed:
0.254 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity

Rose, J.A., Lahiri, S.D., McKinney, D.C., Albert, R., Morningstar, M., Shapiro, A.B., Fisher, S.F., Fleming, P.R.

To be published.

Macromolecule Content

Total Structure Weight: 58.98 kDa
Atom Count: 4,505
Modeled Residue Count: 522
Deposited Residue Count: 522
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A, B	261	Escherichia coli	Mutation(s): 0 Gene Names: map, Z0178, ECs0170 EC: 3.4.11.18
UniProt
Find proteins for P0AE18 (Escherichia coli (strain K12)) Explore P0AE18 Go to UniProtKB: P0AE18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AE18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4L9 Query on 4L9 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	N~2~-[(3,5-difluorophenyl)acetyl]-N-[(3S,7R)-1-methyl-2-oxo-7-phenyl-2,3,4,7-tetrahydro-1H-azepin-3-yl]-L-alaninamide C₂₄ H₂₅ F₂ N₃ O₃ XGCLGFYBNGRVHO-ONGXBYRLSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.305 (Depositor), 0.312 (DCC)
R-Value Work: 0.251 (Depositor), 0.259 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.985	α = 90
b = 62.712	β = 89.59
c = 72.978	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Morningstar, M.

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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