1OB4 | pdb_00001ob4

Cephaibol A

• PDB DOI: https://doi.org/10.2210/pdb1OB4/pdb

• Classification: ANTIBIOTIC
• Organism(s): Emericellopsis tubakii
• Mutation(s): No 


• Deposited: 2003-01-24 Released: 2003-12-11 
• Deposition Author(s): Bunkoczi, G., Schiell, M., Vertesy, L., Sheldrick, G.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.112 (Depositor) 
• R-Value Work: 
  0.103 (DCC) 
• R-Value Observed: 
  0.086 (Depositor) 

Literature

Crystal Structures of Cephaibols

Bunkoczi, G., Schiell, M., Vertesy, L., Sheldrick, G.M.

(2003) J Pept Sci 9: 745

• PubMed: 14658793 
• DOI: https://doi.org/10.1002/psc.496
• Primary Citation Related Structures: 
  1OB4, 1OB6, 1OB7


• PubMed Abstract: 
  

  The crystal structures of the peptaibol antibiotics cephaibol A, cephaibol B and cephaibol C have been determined at ca. 0.9 A resolution. All three adopt a helical conformation with a sharp bend (of about 55 degrees) at the central hydroxyproline. All isovalines were found to possess the D configuration, superposition of all four models (there are two independent molecules in the cephaibol B structure) shows that the N-terminal helix is rigid and the C-terminus is flexible. There are differences in the hydrogen bonding patterns for the three structures that crystallize in different space groups despite relatively similar unit cell dimensions, but only in the case of cephaibol C does the packing emulate the formation of a membrane channel believed to be important for their biological function.

---

Organizational Affiliation: 
• Lehrstuhl für Strukturchemie, Georg-August Universität, Tammannstr. 4, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 1.7 kDa 
• Atom Count: 156 
• Modeled Residue Count: 17 
• Deposited Residue Count: 17 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CEPHAIBOL A	A	17	Emericellopsis tubakii	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	B [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
DIV	A	D-PEPTIDE LINKING	C5 H11 N O2		--
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO
PHL	A	L-PEPTIDE LINKING	C9 H13 N O		PHE

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000156	A	Cephaibol A	Peptaibol / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.112 (Depositor) 
• R-Value Work:  0.103 (DCC) 
• R-Value Observed: 0.086 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.534	α = 90
b = 37.787	β = 90
c = 9.115	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SAINT	data reduction
SADABS	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-11 
Deposition Author(s): Bunkoczi, G., Schiell, M., Vertesy, L., Sheldrick, G.M.

Revision History  

• Version 1.0: 2003-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2018-05-30
  Changes: Data collection
• Version 1.4: 2019-05-22
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary