2XAD

Crystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of teicoplanin

• PDB DOI: https://doi.org/10.2210/pdb2XAD/pdb

• Classification: OXIDOREDUCTASE/ANTIBIOTIC
• Organism(s): Actinoplanes teichomyceticus, Nonomuraea gerenzanensis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-03-31 Released: 2011-03-02 
• Deposition Author(s): Chan, H.C., Huang, Y.T., Lyu, S.Y., Huang, C.J., Li, Y.S., Liu, Y.C., Chou, C.C., Tsai, M.D., Li, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.92 kDa 
• Atom Count: 9,379 
• Modelled Residue Count: 1,060 
• Deposited Residue Count: 1,120 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE	A, B, C, D	273	Actinoplanes teichomyceticus	Mutation(s): 1
UniProt
Find proteins for Q6ZZJ1 (Actinoplanes teichomyceticus) Explore Q6ZZJ1  Go to UniProtKB:  Q6ZZJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TEICOPLANIN	E, F, G, H	7	Nonomuraea gerenzanensis	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth E], N [auth F], R [auth G], V [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	I [auth E], M [auth F], Q [auth G], U [auth H]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
GCS	K [auth E], O [auth F], S [auth G], W [auth H]	2-amino-2-deoxy-beta-D-glucopyranose C6 H13 N O5 MSWZFWKMSRAUBD-QZABAPFNSA-N
T55	L [auth E], P [auth F], T [auth G], X [auth H]	8-METHYLNONANOIC ACID C10 H20 O2 OAOABCKPVCUNKO-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
3MY	E, F, G, H	D-PEPTIDE LINKING	C9 H10 Cl N O3		TYR
OMY	E, F, G, H	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000209	E, F, G, H	Teicoplanin A2-2 beta-D-Glucopyranuronic acid	Glycopeptide / Antibiotic, Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.775	α = 113.89
b = 70.713	β = 108.29
c = 76.313	γ = 98.2

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Chan, H.C., Huang, Y.T., Lyu, S.Y., Huang, C.J., Li, Y.S., Liu, Y.C., Chou, C.C., Tsai, M.D., Li, T.L.

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2012-11-30
  Changes: Other
• Version 1.2: 2014-01-15
  Changes: Database references, Other, Version format compliance
• Version 2.0: 2019-04-24
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary