6XK2 | pdb_00006xk2

Crystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb6XK2/pdb

Classification: TRANSFERASE
Organism(s): Cryptococcus neoformans H99
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-06-25 Released: 2020-07-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.230 (Depositor), 0.233 (DCC)
R-Value Work:
0.181 (Depositor), 0.185 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP

Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 142.31 kDa
Atom Count: 9,325
Modeled Residue Count: 1,266
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D	332	Cryptococcus neoformans H99	Mutation(s): 0 Gene Names: CNAG_02296 EC: 2.7.1.15
UniProt
Find proteins for J9VQ51 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VQ51 Go to UniProtKB: J9VQ51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9VQ51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	F [auth A], I [auth B], L [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D]	G [auth A], J [auth B], N [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth D]