6C6B | pdb_00006c6b

Co-crystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans bound to ADP

PDB DOI: https://doi.org/10.2210/pdb6C6B/pdb

Classification: TRANSFERASE
Organism(s): Cryptococcus neoformans H99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-01-18 Released: 2018-02-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.267 (Depositor), 0.273 (DCC)
R-Value Work:
0.224 (Depositor), 0.227 (DCC)
R-Value Observed:
0.225 (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 Adenylyl-sulfate kinase bound to ADP

Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 142.53 kDa
Atom Count: 9,421
Modeled Residue Count: 1,168
Deposited Residue Count: 1,266
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl-sulfate kinase	A, B, C, D, E A, B, C, D, E, F	211	Cryptococcus neoformans H99	Mutation(s): 0 Gene Names: CNAG_02202 EC: 2.7.1.25
UniProt
Find proteins for J9VMZ3 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VMZ3 Go to UniProtKB: J9VMZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9VMZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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