7XJV | pdb_00007xjv

Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Saccharomyces cerevisiae, Mn/GDP-mannose form

PDB DOI: https://doi.org/10.2210/pdb7XJV/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae W303
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-18 Released: 2023-05-31
Deposition Author(s): Hira, D., Kadooka, C., Oka, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.251 (Depositor), 0.248 (DCC)
R-Value Work:
0.213 (Depositor), 0.216 (DCC)

Starting Model: in silico
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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

Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Saccharomyces cerevisiae, Mn/GDP-mannose form

Hira, D., Kadooka, C., Oka, T.

To be published.

Macromolecule Content

Total Structure Weight: 258.64 kDa
Atom Count: 17,178
Modeled Residue Count: 2,041
Deposited Residue Count: 2,192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,3-mannosyltransferase MNT2	A, B, C, D	548	Saccharomyces cerevisiae W303	Mutation(s): 0 Gene Names: MNT2, YGL257C, NRD558 EC: 2.4.1
UniProt
Find proteins for P53059 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53059 Go to UniProtKB: P53059
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53059
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDD (Subject of Investigation/LOI) Query on GDD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth C] SDF format, chain N [auth B] SDF format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain U [auth C] MOL2 format, chain N [auth B] MOL2 format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain U [auth C] mmCIF format, chain N [auth B] mmCIF format, chain CA [auth D]	CA [auth D], F [auth A], N [auth B], U [auth C]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C₁₆ H₂₅ N₅ O₁₆ P₂ MVMSCBBUIHUTGJ-GDJBGNAASA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D]	DA [auth D] EA [auth D] FA [auth D] G [auth A] GA [auth D] DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain E [auth A] SDF format, chain BA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth D]	BA [auth D], E [auth A], M [auth B], T [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain HA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain AA [auth C]	AA [auth C], HA [auth D], L [auth A], S [auth B], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain S [auth B] Focus chain Z [auth C]