8B4M | pdb_00008b4m

Crystal structure of a hydropyrene synthase (M75L variant) in its closed conformation

PDB DOI: https://doi.org/10.2210/pdb8B4M/pdb

Classification: LYASE
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-09-20 Released: 2023-10-04
Deposition Author(s): Helmer, C.P.O., Driller, R., Loll, B.
Funding Organization(s): German-Israeli Foundation for Research and Development

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.307 (Depositor), 0.310 (DCC)
R-Value Work:
0.252 (Depositor), 0.250 (DCC)
R-Value Observed:
0.255 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A methionine-lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

Ringel, M., Helmer, C.P.O., Zev, S., Driller, R., Buhr, E., Reinbold, M., Schwartz, R., Foley, G., Boden, M., Garbe, D., Schenk, G., Major, D.T., Loll, B., Bruck, T.

(2026) FEBS Lett

DOI: https://doi.org/10.1002/1873-3468.70325

Macromolecule Content

Total Structure Weight: 217.12 kDa
Atom Count: 14,633
Modeled Residue Count: 1,841
Deposited Residue Count: 1,932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase	A, B, C, D, E A, B, C, D, E, F	322	Streptomyces clavuligerus	Mutation(s): 1 Gene Names: SCLAV_p0765 EC: 4.2.3 (PDB Primary Data), 4.2.3.203 (UniProt), 4.2.3.202 (UniProt), 4.2.3.201 (UniProt)
UniProt
Find proteins for D5SK09 (Streptomyces clavuligerus) Explore D5SK09 Go to UniProtKB: D5SK09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5SK09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
212 Query on 212 Download Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain R [auth E] SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain V [auth F] MOL2 format, chain R [auth E] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain V [auth F] mmCIF format, chain R [auth E] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	J [auth B], N [auth D], R [auth E], V [auth F]	ALENDRONATE C₄ H₁₃ N O₇ P₂ OGSPWJRAVKPPFI-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth D] Focus chain R [auth E] Focus chain V [auth F] Interactions & Density Focus chain J [auth B] Focus chain N [auth D] Focus chain R [auth E] Focus chain V [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B] H [auth B] I [auth B] K [auth D] L [auth D] G [auth B], H [auth B], I [auth B], K [auth D], L [auth D], M [auth D], O [auth E], P [auth E], Q [auth E], S [auth F], T [auth F], U [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F]