7WHT | pdb_00007wht

Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in complex with GDP-Mannose

PDB DOI: https://doi.org/10.2210/pdb7WHT/pdb
EM Map EMD-32511: EMDB EMDataResource

Classification: SUGAR BINDING PROTEIN
Organism(s): Leishmania donovani
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-12-31 Released: 2022-10-12
Deposition Author(s): Xu, W., Li, H., Huang, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7WHT

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

Literature

Structural insights into selective inhibition of leishmanial GDP-mannose pyrophosphorylase.

Li, H., Ji, T., Sun, Q., Chen, Y., Xu, W., Huang, C.

(2022) Cell Discov 8: 83-83

PubMed: 36038534 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00424-z
Primary Citation Related Structures:
7WHR, 7WHS, 7WHT

Organizational Affiliation

Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecule Content

Total Structure Weight: 254.46 kDa
Atom Count: 16,980
Modeled Residue Count: 2,160
Deposited Residue Count: 2,274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyl transferase family protein	A, B, C, D, E A, B, C, D, E, F	379	Leishmania donovani	Mutation(s): 0 Gene Names: CGC21_17635 EC: 2.7.7.13
UniProt
Find proteins for E9BG32 (Leishmania donovani) Explore E9BG32 Go to UniProtKB: E9BG32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E9BG32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 G [auth A] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain I [auth B]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C₁₆ H₂₅ N₅ O₁₆ P₂ MVMSCBBUIHUTGJ-GDJBGNAASA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain N [auth D] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain N [auth D] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain N [auth D] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971144
National Natural Science Foundation of China (NSFC)	China	31770807

Revision History (Full details and data files)

Version 1.0: 2022-10-12
Type: Initial release
Version 1.1: 2024-06-26
Changes: Data collection
Version 1.2: 2025-07-02
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.