7Z1I | pdb_00007z1i

Plant myrosinase TGG1 from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb7Z1I/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-02-24 Released: 2023-03-08
Deposition Author(s): Gao, Y., Farmer, E., Jimenez-Sandoval, P., Santiago, J.
Funding Organization(s): European Research Council (ERC), University of Lausanne

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.341 (Depositor), 0.340 (DCC)
R-Value Work:
0.317 (Depositor), 0.320 (DCC)
R-Value Observed:
0.318 (Depositor)

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

Plant myrosinase TGG1 from Arabidopsis thaliana

Gao, Y., Farmer, E., Jimenez-Sandoval, P., Santiago, J.

To be published.

Macromolecule Content

Total Structure Weight: 249.15 kDa
Atom Count: 15,094
Modeled Residue Count: 1,971
Deposited Residue Count: 2,144
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myrosinase 1	A, B, C, D	536	Arabidopsis thaliana	Mutation(s): 0 Gene Names: TGG1, BGLU38, At5g26000, T1N24.7 EC: 3.2.1.147 (PDB Primary Data), 3.2.1.21 (PDB Primary Data)
UniProt
Find proteins for P37702 (Arabidopsis thaliana) Explore P37702 Go to UniProtKB: P37702
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37702
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain CA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain CA [auth D]	AA [auth C] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth C], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain GA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain GA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain GA [auth D]	GA [auth D], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain N [auth A] Interactions & Density Focus chain GA [auth D] Focus chain N [auth A]