8VX3

Crystal structure of a (p)ppApp synthetase from Streptomyces albidoflavus

PDB DOI: https://doi.org/10.2210/pdb8VX3/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces albidoflavus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-03 Released: 2025-02-05
Deposition Author(s): Ahmad, S., Tsang, K.K., Schiefer, V., Kim, Y., Whitney, J.C.
Funding Organization(s): Burroughs Wellcome Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 ?
R-Value Free:
0.276 (Depositor), 0.283 (DCC)
R-Value Work:
0.238 (Depositor), 0.241 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a (p)ppApp synthetase from Streptomyces albidoflavus

Ahmad, S., Tsang, K.K., Schiefer, V., Kim, Y., Whitney, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 90.08 kDa
Atom Count: 6,186
Modelled Residue Count: 801
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apk3	A, B, C, D	207	Streptomyces albidoflavus	Mutation(s): 0 Gene Names: ScoT_12220
UniProt
Find proteins for A0AA37FDV0 (Streptomyces albidoflavus) Explore A0AA37FDV0 Go to UniProtKB: A0AA37FDV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA37FDV0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A], H [auth B], L [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain L [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]