7LKC

Crystal Structure of Keratinimicin A

• PDB DOI: https://doi.org/10.2210/pdb7LKC/pdb

• Classification: ANTIBIOTIC
• Organism(s): Amycolatopsis keratiniphila
• Mutation(s): No 


• Deposited: 2021-02-02 Released: 2022-12-07 
• Deposition Author(s): Davis, K.M., Jeffrey, P.D., Seyedsayamdost, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.168 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Structural and Functional Analysis of Keratinicyclin Reveals Synergistic Antibiosis with Vancomycin against Clostridium difficile

McWhorter, K.L., Chioti, V.T., Xu, F., Jeffrey, P.D., Davis, K.M., Seyedsayamdost, M.R.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.87 kDa 
• Atom Count: 328 
• Modelled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratinimicin A peptide moiety	A, B	7	Amycolatopsis keratiniphila	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose	C [auth G], D [auth K]	2		N/A
Glycosylation Resources
GlyTouCan:  G13233ZQ GlyCosmos:  G13233ZQ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN (Subject of Investigation/LOI)	E [auth A], I [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
YBJ (Subject of Investigation/LOI)	F [auth A], J [auth B]	(2~{S},4~{S},5~{R},6~{S})-4-azanyl-5-methoxy-6-methyl-oxan-2-ol C7 H15 N O3 ZECQVPSAXSIXIC-KQXJUZEQSA-N
FMT (Subject of Investigation/LOI)	G [auth A], K [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMY	A, B	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.168 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 20.72	α = 90
b = 32.251	β = 90
c = 37.941	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Davis, K.M., Jeffrey, P.D., Seyedsayamdost, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	4R00GM129460

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations