9RP0 | pdb_00009rp0

Ensemble refined structure of CotB2 in complex with 2-fluoro-3,7,18-dolabellatriene

PDB DOI: https://doi.org/10.2210/pdb9RP0/pdb

Classification: HYDROLASE
Organism(s): Streptomyces melanosporofaciens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-23 Released: 2025-09-17
Deposition Author(s): Helmer, C.P.O., Loll, B.
Funding Organization(s): German-Israeli Foundation for Research and Development, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.195 (Depositor), 0.207 (DCC)
R-Value Work:
0.165 (Depositor), 0.181 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6GGI

Literature

Ensemble refined structure of CotB2 in complex with 2-fluoro-3,7,18-dolabellatriene

Helmer, C.P.O., Loll, B.

To be published.

Macromolecule Content

Total Structure Weight: 75.99 kDa
Atom Count: 5,171
Modeled Residue Count: 594
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclooctat-9-en-7-ol synthase	A, B	318	Streptomyces melanosporofaciens	Mutation(s): 0 Gene Names: CotB2 EC: 4.2.3.146
UniProt
Find proteins for C9K1X5 (Streptomyces melanosporofaciens) Explore C9K1X5 Go to UniProtKB: C9K1X5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C9K1X5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B]	N [auth A], X [auth B]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain X [auth B]
EXW Query on EXW Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain U [auth B] MOL2 format, chain I [auth A] MOL2 format, chain U [auth B] mmCIF format, chain I [auth A] mmCIF format, chain U [auth B]	I [auth A], U [auth B]	2-fluoro-3,7,18-dolabellatriene C₂₀ H₃₁ F WCSSNSDHTDBDFK-PWWCRXLASA-N		Interactions Focus chain I [auth A] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain U [auth B]
PPV Query on PPV Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain T [auth B] mmCIF format, chain H [auth A] mmCIF format, chain T [auth B]	H [auth A], T [auth B]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain T [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B]	J [auth A], V [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth A] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain V [auth B]
CCN Query on CCN Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	ACETONITRILE C₂ H₃ N WEVYAHXRMPXWCK-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	O [auth A], Y [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain W [auth B]	K [auth A], L [auth A], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]