2J9A

blLAP in Complex with Microginin FR1

PDB DOI: https://doi.org/10.2210/pdb2J9A/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Bos taurus, Microcystis sp.
Mutation(s): No

Deposited: 2006-11-06 Released: 2006-12-06
Deposition Author(s): Kraft, M., Schleberger, C., Weckesser, J., Schulz, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.173
R-Value Work: 0.145
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Binding Structure of the Leucine Aminopeptidase Inhibitor Microginin Fr1.

Kraft, M., Schleberger, C., Weckesser, J., Schulz, G.E.

(2006) FEBS Lett 580: 6943

PubMed: 17157838 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2006.11.060
Primary Citation of Related Structures:
2J9A

PubMed Abstract:
Natural bioactive compounds are of general interest for pharmaceutical research because they may serve as leads in drug development campaigns. Among them, microginins are linear peptides known to inhibit various exopeptidases. The crystal structure of microginin FR1 from Microcystis sp. bound to bovine lens leucine aminopeptidase was established at 1.73 Angstrom resolution. The observed binding structure could be beneficial for the design of potent aminopeptidase inhibitors.

Organizational Affiliation

Institut für Biologie II, Microbiologie, Albert-Ludwigs-Universität, Schänzlestr. 1, D-79104 Freiburg im Breisgau, Germany.

Macromolecule Content

Total Structure Weight: 54.38 kDa
Atom Count: 4,501
Modelled Residue Count: 489
Deposited Residue Count: 491
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOSOL AMINOPEPTIDASE	A	487	Bos taurus	Mutation(s): 0 EC: 3.4.11.1 (PDB Primary Data), 3.4.11.5 (PDB Primary Data)
UniProt
Find proteins for P00727 (Bos taurus) Explore P00727 Go to UniProtKB: P00727
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00727
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MICROGININ FR1	B [auth D]	4	Microcystis sp.	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHY Query on AHY Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D]	K [auth D]	(2S,3R)-3-AMINO-2-HYDROXYDECANOIC ACID C₁₀ H₂₁ N O₃ CZHBZYFMCYCASB-BDAKNGLRSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	G [auth A], H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A]	I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLE Query on MLE	B [auth D]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000705 Query on PRD_000705	B [auth D]	MICROGININ FR1	Peptide-like / Inhibitor		Interactions Focus chain B [auth D] Interactions & Density Focus chain B [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.173
R-Value Work: 0.145
R-Value Observed: 0.146
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.982	α = 90
b = 129.982	β = 90
c = 120.813	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-12-06
Type: Initial release
Version 1.1: 2012-09-05
Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2012-11-30
Changes: Other
Version 1.3: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description