3TBH | pdb_00003tbh

Crystal structure of O-Acetyl Serine Sulfhydrylase in complex with octapeptide derived from Serine Acetyl Transferase of Leishmania donovani

• PDB DOI: https://doi.org/10.2210/pdb3TBH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Leishmania donovani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-06 Released: 2012-08-01 
• Deposition Author(s): Raj, I., Gourinath, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.220 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of O-Acetyl Serine Sulfhydrylase in complex with octapeptide derived from Serine Acetyl Transferase of Leishmania donovani

Raj, I., Kumar, S., Gourinath, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 36.78 kDa 
• Atom Count: 2,622 
• Modeled Residue Count: 323 
• Deposited Residue Count: 342 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-acetyl serine sulfhydrylase	A	334	Leishmania donovani	Mutation(s): 0  Gene Names: ldOASS, OASS EC: 2.5.1.47
UniProt
Find proteins for G1C2I2 (Leishmania donovani) Explore G1C2I2  Go to UniProtKB:  G1C2I2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine acetyl transferase derived octapeptide	B	8	Leishmania donovani	Mutation(s): 0  EC: 2.3.1.30
UniProt
Find proteins for E9BR69 (Leishmania donovani) Explore E9BR69  Go to UniProtKB:  E9BR69

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.220 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.217	α = 90
b = 62.44	β = 90
c = 43.538	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Raj, I., Gourinath, S.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection