8QWS | pdb_00008qws

Crystal structure of CotB2 variant V80L in complex with alendronate

PDB DOI: https://doi.org/10.2210/pdb8QWS/pdb

Classification: LYASE
Organism(s): Streptomyces melanosporofaciens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-10-20 Released: 2024-04-24
Deposition Author(s): Dimos, N., Himpich, S., Ringel, M., Driller, R., Major, D.T., Brueck, T., Loll, B.
Funding Organization(s): German-Israeli Foundation for Research and Development

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.205 (Depositor), 0.204 (DCC)
R-Value Work:
0.172 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

How Can the Diterpene Synthase CotB2V80L Alter the Product Profile?

Himpich, S., Ringel, M., Schwartz, R., Dimos, N., Driller, R., Helmer, C.P.O., Kumar Gupta, P., Haack, M., Thomas Major, D., Bruck, T., Loll, B.

(2024) ChemCatChem n/a

DOI: https://doi.org/10.1002/cctc.202400711

Macromolecule Content

Total Structure Weight: 75.96 kDa
Atom Count: 5,440
Modeled Residue Count: 573
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C9K1X5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHD (Subject of Investigation/LOI) Query on AHD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain S [auth B]	C [auth A], S [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 S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain Q [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain Q [auth A]	FA [auth B], Q [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain FA [auth B] Focus chain Q [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth B]	BA [auth B], GA [auth B], HA [auth B], J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain BA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain J [auth A] Interactions & Density Focus chain BA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain G [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain G [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain G [auth A]	CA [auth B] EA [auth B] G [auth A] H [auth A] I [auth A] CA [auth B], EA [auth B], G [auth A], H [auth A], I [auth A], K [auth A], M [auth A], N [auth A], R [auth A], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain EA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DA [auth B] SDF format, chain L [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	AA [auth B], DA [auth B], L [auth A], O [auth A], P [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain O [auth A] Focus chain P [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [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 T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	D [auth A] E [auth A] F [auth A] T [auth B] U [auth B] D [auth A], E [auth A], F [auth A], T [auth B], U [auth B], V [auth B], W [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 T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]