3IP1 | pdb_00003ip1

Structure of putative alcohol dehydrogenase (TM_042) from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3IP1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-15 Released: 2009-09-29 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structure of putative alcohol dehydrogenase (TM_042) from Thermotoga maritima

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

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: 180.46 kDa 
• Atom Count: 12,840 
• Modeled Residue Count: 1,583 
• Deposited Residue Count: 1,616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase, zinc-containing	A, B, C, D	404	Thermotoga maritima	Mutation(s): 0  Gene Names: TM_0412, TM_0422 EC: 1.1.1
UniProt
Find proteins for Q9WYP3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYP3  Go to UniProtKB:  Q9WYP3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A], F [auth A], H [auth B], I [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], J [auth B], N [auth C], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.365	α = 90
b = 131.555	β = 90
c = 161.559	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
PHENIX	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary