9RP1 | pdb_00009rp1

Ensemble refined structure of CotB2 in complex with alendronate

PDB DOI: https://doi.org/10.2210/pdb9RP1/pdb

Classification: HYDROLASE
Organism(s): Streptomyces melanosporofaciens
Expression System: Escherichia coli DH5[alpha]
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: 2.10 Å
R-Value Free:
0.212 (Depositor), 0.229 (DCC)
R-Value Work:
0.173 (Depositor), 0.189 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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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.

Re-refinement Note

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

Literature

Ensemble refined structure of CotB2 in complex with alendronate

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

To be published.

Macromolecule Content

Total Structure Weight: 74.18 kDa
Atom Count: 4,979
Modeled Residue Count: 579
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHD Query on AHD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE C₄ H₉ N O₇ P₂ OGSPWJRAVKPPFI-UHFFFAOYSA-J		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]