8WVT | pdb_00008wvt

Crystal structure of Lsd18 in complex with ligands

PDB DOI: https://doi.org/10.2210/pdb8WVT/pdb

Classification: FLAVOPROTEIN
Organism(s): Streptomyces lasalocidi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-24 Released: 2024-11-06
Deposition Author(s): Deng, Y.M., Hu, Y.L., Chen, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.208 (Depositor), 0.208 (DCC)
R-Value Observed:
0.210 (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.

Literature

Crystal structure of Lsd18 in complex with ligands

Deng, Y.M., Hu, Y.L., Chen, X.

To be published.

Macromolecule Content

Total Structure Weight: 108.2 kDa
Atom Count: 7,861
Modeled Residue Count: 936
Deposited Residue Count: 976
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative epoxidase LasC	A, B	488	Streptomyces lasalocidi	Mutation(s): 0 Gene Names: lsd18 EC: 1.14.13
UniProt
Find proteins for B5M9L6 (Streptomyces lasalocidi) Explore B5M9L6 Go to UniProtKB: B5M9L6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5M9L6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
X9E (Subject of Investigation/LOI) Query on X9E Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(4R,5S)-3-((2R,3S,4S,E)-2,6-diethyl-9-((2R,3R)-2-ethyl-3-methyloxiran-2-yl)-3-hydroxy-4-methylnon-6-enoyl)-4-methyl-5-phenyloxazolidin-2-one C₂₉ H₄₃ N O₅ MAKHZPRKABYPIS-LKCQFNNRSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
A1LWM (Subject of Investigation/LOI) Query on A1LWM Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	(4R,5S)-4-methyl-5-phenyl-3-((2R,3S,4S,6E,10E)-2,6,10-triethyl-3-hydroxy-4-methyldodeca-6,10-dienoyl)oxazolidin-2-one C₂₉ H₄₃ N O₄ GIEHXLSOYWFSMM-FYYHNBHTSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
DMS (Subject of Investigation/LOI) Query on DMS Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]