6XBT

Streptomyces coelicolor methylmalonyl-CoA epimerase (Q60A) in complex with 2-nitronate-propionyl-CoA

PDB DOI: https://doi.org/10.2210/pdb6XBT/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: 1.49 Å
R-Value Free: 0.184
R-Value Work: 0.170
R-Value Observed: 0.171

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 (Q60A) 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: 17.89 kDa
Atom Count: 1,468
Modelled Residue Count: 140
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]
COA Query on COA 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]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [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]