7V3E

The complex structure of soBcmB and its intermediate product 1a

PDB DOI: https://doi.org/10.2210/pdb7V3E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces ossamyceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-10 Released: 2023-02-15
Deposition Author(s): Wu, L., Zhou, J.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.229
R-Value Work: 0.217
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of SoBcmB and its side way intermediate product

Wu, L., Zhou, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 113.38 kDa
Atom Count: 7,013
Modelled Residue Count: 840
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dioxygenase	A, B, C	328	Streptomyces ossamyceticus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5WI Query on 5WI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain L [auth C]	E [auth A], G [auth B], L [auth C]	(3S,6Z)-3-[(2S)-butan-2-yl]-6-[(2R)-2-methyl-2,3-bis(oxidanyl)propylidene]piperazine-2,5-dione C₁₂ H₂₀ N₂ O₄ KGPSCQPJVWXIGR-PMSMWWAASA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C]
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C]	D [auth A], H [auth B], M [auth C]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain M [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C]	F [auth A], I [auth B], N [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]