OCA Atlas for 1P8K

1P8K

Hydrolase Dna

date

May 07, 2003

title

The Structure And Dna Recognition Of A Bifunctional Homing Endonuclease And Group I Intron Splicing Factor

authors

B.L.Stoddard, J.M.Bolduc

compound

source

Molecule: 5'- D(Pgpcpgpcpgpcptpgpapgpgpapgpgptptptpc)- 3';
Chain: A
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Ptpcptpgptpapapapgpcpgpcpa)-3'
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: 5'- D(Pgpcpgpcptptptpapcpapgpapgpapapa)-3';
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: 5'- D(Pcpcptpcpcptpcpapgpcpgpcpgpcpt)-3';
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Intron-Encoded Endonuclease I-Anii
Chain: Z
Synonym: Mrna Maturase Bi1, Cob Intron Protein
Ec: 3.1.-.-
Engineered: Yes

Organism_scientific: Emericella Nidulans
Organism_taxid: 162425
Gene: Aspergillus Nidulans
Expression_system: Escherichia Coli
Expression_system_taxid: 562

symmetry

Space Group: P 1 21 1

R_factor

0.239

R_Free

0.264

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
60.462	72.841	65.231	90.00	108.21	90.00

method

X-Ray Diffraction

resolution

2.60 Å

ligand

MG, MSE

enzyme

Hydrolase E.C.3.1 BRENDA

Gene
Ontology

Chain	Function	Process	Component
Z

Primary reference

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor., Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL, Genes Dev 2003 Dec 1;17(23):2875-88. Epub 2003 Nov 21. PMID:14633971

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]

Biological Unit Coordinates (1p8k.pdb1.gz) 68 Kb

LPC: Ligand-Protein Contacts for 1P8K

CSU: Contacts of Structural Units for 1P8K

Likely Quarternary Molecular Structure file(s) for 1P8K

Structure Factors (233 Kb)

Retrieve 1P8K in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1P8K from S2C, [Save to disk]

Re-refined 1p8k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1P8K 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 1P8K

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 1P8K, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1p8kz1, region Z:1-125 [Jmol] [rasmolscript] [script source]
- Domain d1p8kz2, region Z:126-254 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1p8k_B] [1p8k] [1p8k_D] [1p8k_A] [1p8k_Z] [1p8k_C]

SWISS-PROT database: [P03880]

Domain organization of [ANI1_EMENI] by SWISSPFAM

Other resources with information on 1P8K

Community annotation for 1P8K 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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