OCA Atlas for 5NPP

5NPP

Isomerase

date

Apr 18, 2017

title

2.22a Structure Of Thiophene2 And Gsk945237 With S.Aureus Dn And Dna

authors

B.D.Bax, P.F.Chan, R.A.Stavenger

compound

source

Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B,Dna Gyr Subunit A;
Chain: B, D
Ec: 5.99.1.3,5.99.1.3,5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 158879
Strain: N315
Gene: Gyrb, Sa0005, Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Apgpcpcpgptpapgpgptpapcpcptpapcpgpgpcp
Chain: E, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Apgpcpcpgptpapgpgptpapcpcptpapcpgpgpcp
Chain: A, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

symmetry

Space Group: P 61

R_factor

0.182

R_Free

0.227

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
92.850	92.850	409.980	90.00	90.00	120.00

method

X-Ray Diffraction

resolution

2.22 Å

ligand

6EJ, 94K, DMS, GOL, MN, NA

enzyme

Isomerase E.C.5.99.1.3 BRENDA

Gene
Ontology

Chain	Function	Process	Component
D, B

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (269 Kb) [Save to disk]

Biological Unit Coordinates (5npp.pdb1.gz) 261 Kb

LPC: Ligand-Protein Contacts for 5NPP

CSU: Contacts of Structural Units for 5NPP

Structure Factors (1454 Kb)

Retrieve 5NPP in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5NPP from S2C, [Save to disk]

Re-refined 5npp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5NPP 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 5NPP

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5npp_D] [5npp_B] [5npp_F] [5npp_C] [5npp_E] [5npp_A]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 5NPP

Community annotation for 5NPP at PDBWiki (http://pdbwiki.org)

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