OCA Atlas for 1EEX

1EEX

Lyase

date

Feb 04, 2000

title

Crystal Structure Of The Diol Dehydratase-Adeninylpentylcoba Complex From Klebsiella Oxytoca

authors

N.Shibata, J.Masuda, T.Toraya, Y.Morimoto, N.Yasuoka

compound

source

Molecule: Propanediol Dehydratase
Chain: A, L
Fragment: Alpha Chain
Ec: 4.2.1.28
Engineered: Yes

Organism_scientific: Klebsiella Oxytoca
Organism_taxid: 571
Atcc: Atcc8724
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc119

Molecule: Propanediol Dehydratase
Chain: B, E
Fragment: Beta Chain
Ec: 4.2.1.28
Engineered: Yes

Molecule: Propanediol Dehydratase
Chain: G, M
Fragment: Gamma Chain
Ec: 4.2.1.28
Engineered: Yes

symmetry

Space Group: P 21 21 21

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
73.380	121.400	207.600	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

1.70 Å

ligand

COY, K, PGO

enzyme

Lyase E.C.4.2.1.28 BRENDA

related structures

by homologous chain: 1EGV

Gene
Ontology

Chain	Function	Process	Component
A, L
M, G, E, B

Primary reference

How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex., Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N, Structure Fold Des 2000 Jul 15;8(7):775-88. PMID:10903944

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (316 Kb) [Save to disk]

Biological Unit Coordinates (1eex.pdb1.gz) 308 Kb

LPC: Ligand-Protein Contacts for 1EEX

CSU: Contacts of Structural Units for 1EEX

Likely Quarternary Molecular Structure file(s) for 1EEX

Structure Factors (1489 Kb)

Retrieve 1EEX in mmCIF format [Save to disk]

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

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

View 1EEX 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 1EEX

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 1EEX, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1eexa_, region A [Jmol] [rasmolscript] [script source]
- Domain d1eexb_, region B [Jmol] [rasmolscript] [script source]
- Domain d1eexe_, region E [Jmol] [rasmolscript] [script source]
- Domain d1eexg_, region G [Jmol] [rasmolscript] [script source]
- Domain d1eexl_, region L [Jmol] [rasmolscript] [script source]
- Domain d1eexm_, region M [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: [1eex_G] [1eex_A] [1eex] [1eex_B] [1eex_M] [1eex_L] [1eex_E]

SWISS-PROT database: [Q59470] [Q59471] [Q59472]

Domain organization of [Q59470_KLEOX] [Q59471_KLEOX] [Q59472_KLEOX] by SWISSPFAM

Other resources with information on 1EEX

Community annotation for 1EEX 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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