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 1.0 of the entry. See complete history.

Literature

crystal structure of s hydropyrene synthase in its closed conformation

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

To be published.

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 J [auth B] SDF format, chain N [auth D] SDF format, chain R [auth E] SDF format, chain V [auth F] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain R [auth E] MOL2 format, chain V [auth F] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain R [auth E] mmCIF format, chain V [auth F]	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 G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth F] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F]	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]