8OT2 | pdb_00008ot2

Structural and functional studies of geldanamycin amide synthase ShGdmF

PDB DOI: https://doi.org/10.2210/pdb8OT2/pdb

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

Deposited: 2023-04-20 Released: 2024-05-01
Deposition Author(s): Ewert, W., Zeilinger, C., Kirschning, A., Preller, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.185 (Depositor), 0.183 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (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

Structural and functional studies of geldanamycin amide synthase ShGdmF

Ewert, W., Bartens, C., Heutling, A., Ongouta, J., Vogt, M., Kishore, A., Zeilinger, C., Preller, M.

To be published.

Macromolecule Content

Total Structure Weight: 31.11 kDa
Atom Count: 2,054
Modeled Residue Count: 237
Deposited Residue Count: 263
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GdmF	A	263	Streptomyces hygroscopicus	Mutation(s): 0 Gene Names: gdmF
UniProt
Find proteins for Q84G21 (Streptomyces hygroscopicus) Explore Q84G21 Go to UniProtKB: Q84G21
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84G21
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W0E (Subject of Investigation/LOI) Query on W0E Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	3-azanyl-5-methyl-phenol C₇ H₉ N O NCUABBHFJSFKOJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain K [auth A] MOL2 format, chain S [auth A] MOL2 format, chain K [auth A] mmCIF format, chain S [auth A] mmCIF format, chain K [auth A]	K [auth A], S [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain S [auth A] Interactions & Density Focus chain K [auth A] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain B [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain B [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain B [auth A]	B [auth A] G [auth A] H [auth A] I [auth A] M [auth A] B [auth A], G [auth A], H [auth A], I [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain R [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain R [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] J [auth A] L [auth A] C [auth A], D [auth A], E [auth A], J [auth A], L [auth A], R [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain R [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain R [auth A]