3L77 | pdb_00003l77

X-ray structure alcohol dehydrogenase from archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP

• PDB DOI: https://doi.org/10.2210/pdb3L77/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermococcus sibiricus MM 739
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-28 Released: 2011-01-19 
• Deposition Author(s): Lyashenko, A.V., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.180 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

X-ray structure alcohol dehydrogenase from archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP

Lyashenko, A.V., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 28.31 kDa 
• Atom Count: 2,268 
• Modeled Residue Count: 235 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain alcohol dehydrogenase	A	235	Thermococcus sibiricus MM 739	Mutation(s): 0  Gene Names: TSIB_0319 EC: 1.1.1.2
UniProt
Find proteins for C6A190 (Thermococcus sibiricus (strain DSM 12597 / MM 739)) Explore C6A190  Go to UniProtKB:  C6A190

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NJP	B [auth A]	5-hydroxy-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H29 N7 O18 P3 PDVSLSLEJOIQNF-NNYOXOHSSA-O
PG4	D [auth A], F [auth A], M [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	C [auth A], E [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.180 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.62	α = 90
b = 83.23	β = 90
c = 120.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Lyashenko, A.V., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-04-03
  Changes: Derived calculations, Refinement description
• Version 1.3: 2017-09-27
  Changes: Data collection
• Version 1.4: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.5: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-10-16
  Changes: Structure summary