5YQB

Crystal structure of E.coli aminopeptidase N in complex with Puromycin

PDB DOI: https://doi.org/10.2210/pdb5YQB/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-06 Released: 2018-11-14
Deposition Author(s): Marapaka, A.K., Ganji, R.J., Reddi, R., Addlagatta, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.182
R-Value Work: 0.161
R-Value Observed: 0.162

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Puromycin, a selective inhibitor of PSA acts as a substrate for other M1 family aminopeptidases: Biochemical and structural basis

Reddi, R., Ganji, R.J., Marapaka, A.K., Bala, S.C., Yerra, N.V., Haque, N., Addlagatta, A.

(2020) Int J Biol Macromol 165: 1373-1381

DOI: https://doi.org/10.1016/j.ijbiomac.2020.10.035

Macromolecule Content

Total Structure Weight: 101.98 kDa
Atom Count: 7,949
Modelled Residue Count: 866
Deposited Residue Count: 891
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A	891	Escherichia coli K-12	Mutation(s): 0 Gene Names: pepN, b0932, JW0915 EC: 3.4.11.2
UniProt
Find proteins for P04825 (Escherichia coli (strain K12)) Explore P04825 Go to UniProtKB: P04825
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04825
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GMC Query on GMC 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]	(2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL C₁₂ H₁₈ N₆ O₃ RYSMHWILUNYBFW-GRIPGOBMSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
0A1 Query on 0A1 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]	O-methyl-L-tyrosine C₁₀ H₁₃ N O₃ GEYBMYRBIABFTA-VIFPVBQESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.182
R-Value Work: 0.161
R-Value Observed: 0.162
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.292	α = 90
b = 120.292	β = 90
c = 170.123	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-14
Type: Initial release
Version 1.1: 2022-07-27
Changes: Database references, Refinement description
Version 1.2: 2023-11-22
Changes: Data collection, Refinement description

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Help and Resources

5YQB

Crystal structure of E.coli aminopeptidase N in complex with Puromycin

Puromycin, a selective inhibitor of PSA acts as a substrate for other M1 family aminopeptidases: Biochemical and structural basis

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)