OCA Atlas for 1OK4

1OK4

Lyase

date

Jul 17, 2003

title

Archaeal Fructose 1,6-Bisphosphate Aldolase Covalently Bound Substrate Dihydroxyacetone Phosphate

authors

E.Lorentzen, P.Zwart, A.Stark, R.Hensel, B.Siebers, E.Pohl

compound

source

Molecule: Fructose-Bisphosphate Aldolase Class I
Chain: A, B, C, D, E, F, G, H, I, J
Synonym: Fbp Aldolase
Ec: 4.1.2.13
Engineered: Yes
Other_details: Lys177 Schiff-Base With Dhap

Organism_scientific: Thermoproteus Tenax
Organism_taxid: 2271
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_plasmid: Pet15b

symmetry

Space Group: P 1 21 1

R_factor

0.163

R_Free

0.185

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
82.400	157.300	101.500	90.00	108.20	90.00

method

X-Ray Diffraction

resolution

2.10 Å

ligand

13P

enzyme

Lyase E.C.4.1.2.13 BRENDA

related structures

by homologous chain: 1OK6, 1W8R

Gene
Ontology

Chain	Function	Process	Component
F, A, J, E, B, H, C, D, I, G

Primary reference

Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins., Lorentzen E, Pohl E, Zwart P, Stark A, Russell RB, Knura T, Hensel R, Siebers B, J Biol Chem 2003 Nov 21;278(47):47253-60. Epub 2003 Aug 26. PMID:12941964

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (398 Kb) [Save to disk]

Biological Unit Coordinates (1ok4.pdb1.gz) 198 Kb

Biological Unit Coordinates (1ok4.pdb2.gz) 199 Kb

LPC: Ligand-Protein Contacts for 1OK4

CSU: Contacts of Structural Units for 1OK4

Likely Quarternary Molecular Structure file(s) for 1OK4

Structure Factors (1799 Kb)

Retrieve 1OK4 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1OK4 from S2C, [Save to disk]

Re-refined 1ok4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1OK4 in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1OK4

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1OK4, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1ok4a_, region A [Jmol] [rasmolscript] [script source]
- Domain d1ok4b_, region B [Jmol] [rasmolscript] [script source]
- Domain d1ok4c_, region C [Jmol] [rasmolscript] [script source]
- Domain d1ok4d_, region D [Jmol] [rasmolscript] [script source]
- Domain d1ok4e_, region E [Jmol] [rasmolscript] [script source]
- Domain d1ok4f_, region F [Jmol] [rasmolscript] [script source]
- Domain d1ok4g_, region G [Jmol] [rasmolscript] [script source]
- Domain d1ok4h_, region H [Jmol] [rasmolscript] [script source]
- Domain d1ok4i_, region I [Jmol] [rasmolscript] [script source]
- Domain d1ok4j_, region J [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ok4_H] [1ok4_E] [1ok4_G] [1ok4_D] [1ok4_I] [1ok4_B] [1ok4_F] [1ok4_J] [1ok4] [1ok4_C] [1ok4_A]

SWISS-PROT database: [P58315]

Domain organization of [ALF1_THETE] by SWISSPFAM

Domain found in 1OK4: [DeoC ] by SMART

Other resources with information on 1OK4

Community annotation for 1OK4 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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