9RP2 | pdb_00009rp2

Ensemble refined structure of CotB2 F107A in complex with alendronate

PDB DOI: https://doi.org/10.2210/pdb9RP2/pdb

Classification: HYDROLASE
Organism(s): Streptomyces melanosporofaciens
Expression System: Escherichia coli DH5[alpha]
Mutation(s): Yes

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: 1.93 Å
R-Value Free:
0.216 (Depositor), 0.232 (DCC)
R-Value Work:
0.179 (Depositor), 0.191 (DCC)
R-Value Observed:
0.181 (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: 7AO0

Literature

Ensemble refined structure of CotB2 F107A in complex with alendronate

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

To be published.

Macromolecule Content

Total Structure Weight: 74.57 kDa
Atom Count: 5,238
Modeled Residue Count: 591
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): 1 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHD Query on AHD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B]	D [auth A], O [auth B]	4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE C₄ H₉ N O₇ P₂ OGSPWJRAVKPPFI-UHFFFAOYSA-J		Interactions Focus chain D [auth A] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth B]	C [auth A], E [auth A], J [auth B], P [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B]	I [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]