6TSP | pdb_00006tsp

Marasmius oreades agglutinin (MOA) inhibited by zinc

PDB DOI: https://doi.org/10.2210/pdb6TSP/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Marasmius oreades
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-12-21 Released: 2020-08-05
Deposition Author(s): Cordara, G., Manna, D., Krengel, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.235 (Depositor), 0.238 (DCC)
R-Value Work:
0.207 (Depositor), 0.213 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of MOA in complex with a peptide fragment: a protease caught in flagranti

Manna, D., Cordara, G., Krengel, U.

(2020) Curr Res Struct Biol 2: 56-67

DOI: https://doi.org/10.1016/j.crstbi.2020.04.003

Macromolecule Content

Total Structure Weight: 34.71 kDa
Atom Count: 2,623
Modeled Residue Count: 292
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin	A [auth AAA]	293	Marasmius oreades	Mutation(s): 0
UniProt
Find proteins for Q8X123 (Marasmius oreades) Explore Q8X123 Go to UniProtKB: Q8X123
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8X123
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose	B [auth A], C [auth B]	3		N/A	Interactions Focus chain B [auth A] Focus chain C [auth B] Interactions & Density Focus chain B [auth A] Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G47548GA GlyCosmos: G47548GA GlyGen: G47548GA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	D [auth C]	3		N/A	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G11065GA GlyCosmos: G11065GA GlyGen: G11065GA

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA], I [auth AAA], J [auth AAA]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Interactions & Density Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain R [auth AAA] SDF format, chain S [auth AAA] SDF format, chain P [auth AAA] SDF format, chain N [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain N [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain N [auth AAA]	N [auth AAA] O [auth AAA] P [auth AAA] Q [auth AAA] R [auth AAA] N [auth AAA], O [auth AAA], P [auth AAA], Q [auth AAA], R [auth AAA], S [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Interactions & Density Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA], F [auth AAA], G [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA]	L [auth AAA], M [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth AAA] Focus chain M [auth AAA] Interactions & Density Focus chain L [auth AAA] Focus chain M [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth AAA] MOL2 format, chain K [auth AAA] mmCIF format, chain K [auth AAA]	K [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Interactions & Density Focus chain K [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.235 (Depositor), 0.238 (DCC)
R-Value Work: 0.207 (Depositor), 0.213 (DCC)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.071	α = 90
b = 121.071	β = 90
c = 99.624	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Cordara, G.

Manna, D.

Krengel, U.

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description