6XBS | pdb_00006xbs

Streptomyces coelicolor methylmalonyl-CoA epimerase (E43Q) in complex with 2-nitronate-propionyl-CoA

PDB DOI: https://doi.org/10.2210/pdb6XBS/pdb

Classification: ISOMERASE/INHIBITOR
Organism(s): Streptomyces coelicolor A3(2)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-06-07 Released: 2020-07-01
Deposition Author(s): Stunkard, L.M., Boram, T.J., Benjamin, A.B., Bower, J.B., Lohman, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.179 (Depositor), 0.183 (DCC)
R-Value Work:
0.152 (Depositor), 0.161 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Streptomyces coelicolor methylmalonyl-CoA epimerase (E43Q) in complex with 2-nitronate-propionyl-CoA

Stunkard, L.M., Boram, T.J., Benjamin, A.B., Bower, J.B., Lohman, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 17.12 kDa
Atom Count: 1,505
Modeled Residue Count: 140
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonyl-CoA epimerase	A	146	Streptomyces coelicolor A3(2)	Mutation(s): 2 Gene Names: SCO5398
UniProt
Find proteins for Q9L2C2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9L2C2 Go to UniProtKB: Q9L2C2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9L2C2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KFV (Subject of Investigation/LOI) Query on KFV Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	[1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium C₂₄ H₃₈ N₈ O₁₉ P₃ S BLWVPDVKNPMTPY-ZSJPKINUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]