8WWW | pdb_00008www

Crystal structure of the adenylation domain of SyAstC

PDB DOI: https://doi.org/10.2210/pdb8WWW/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces yokosukanensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-27 Released: 2024-06-05
Deposition Author(s): Li, Z., Zhu, Z., Zhu, D., Shen, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.262 (Depositor), 0.262 (DCC)
R-Value Work:
0.191 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Functional Application of the Single-Module NRPS-like d-Alanyltransferase in Maytansinol Biosynthesis

Li, Z., Zhu, Z., Xu, G., Wei, L., Liu, J., Wang, H., Lu, C., Li, Y., Zhu, D., Shen, Y.

(2024) ACS Catal 14: 8062-8072

DOI: https://doi.org/10.1021/acscatal.4c00082

Macromolecule Content

Total Structure Weight: 109.61 kDa
Atom Count: 7,715
Modeled Residue Count: 998
Deposited Residue Count: 1,002
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carrier domain-containing protein	A, B	501	Streptomyces yokosukanensis	Mutation(s): 0 Gene Names: AQI95_26035
UniProt
Find proteins for A0A124HF73 (Streptomyces yokosukanensis) Explore A0A124HF73 Go to UniProtKB: A0A124HF73
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A124HF73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YG3 (Subject of Investigation/LOI) Query on YG3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-[(2R)-2-azanylpropanoyl]sulfamate C₁₃ H₁₉ N₇ O₇ S CWWYMWDIYBJVLP-ZOBJURTISA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]