1HHF | pdb_00001hhf

Decaplanin second P6122-Form

• PDB DOI: https://doi.org/10.2210/pdb1HHF/pdb

• Classification: ANTIBIOTIC
• Organism(s): uncultured actinomycete
• Mutation(s): No 


• Deposited: 2000-12-22 Released: 2005-07-11 
• Deposition Author(s): Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.211 (Depositor) 
• R-Value Work: 
  0.168 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structures of Four Crystal Forms of Decaplanin

Lehmann, C., Debreczeni, J.E., Bunkoczi, G., Dauter, M., Dauter, Z., Vertesy, L., Sheldrick, G.M.

(2003) Helvetica Chim Acta 86: 1478

• DOI: https://doi.org/10.1002/HLCA.200390131

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.74 kDa 
• Atom Count: 548 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DECAPLANIN	A, B, C, D	7	uncultured actinomycete	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G13233ZQ GlyCosmos:  G13233ZQ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ERE	I [auth A], L [auth B], M [auth C], R [auth D]	4-epi-vancosamine C7 H15 N O3 OIJZDPGKNVKVBL-VZFHVOOUSA-N
PO4	P [auth C], Q [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	J [auth A], K [auth A], N [auth C], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMX	A, B, C, D	L-PEPTIDE LINKING	C9 H11 N O4		TYR

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000207	A, B, C, D	Decaplanin	Glycopeptide / Antibiotic

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000207	E, F, G, H	Decaplanin	Glycopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.211 (Depositor) 
• R-Value Work:  0.168 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.101	α = 90
b = 60.101	β = 90
c = 131.387	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHARP	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-11 
Deposition Author(s): Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

Revision History  

• Version 1.0: 2005-07-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2012-07-11
  Changes: Other
• Version 1.3: 2012-11-30
  Changes: Other
• Version 1.4: 2013-05-01
  Changes: Non-polymer description
• Version 2.0: 2019-04-24
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2019-07-10
  Changes: Data collection
• Version 2.2: 2019-07-24
  Changes: Data collection
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 3.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary