OCA Atlas for 2GPM

2GPM

Rna

date

Apr 18, 2006

title

Crystal Structure Of An Rna Racemate

authors

W.Rypniewski, M.Vallazza, M.Perbandt, S.Klussmann, C.Betzel, V.A.

compound

source

Molecule: Rna (5'-R((0c)P(0u)P(0g)P(0g)P(0g)P(0c)P(0 3');
Chain: K, M
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Is A 'Spiegelmer' And Occurs I From Thermus Flavus;

Molecule: Rna (5'-R((0c)P(0c)P(0g)P(0c)P(0c)P(0u)P(0 3');
Chain: L, N
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Is A 'Spiegelmer' And Occurs I From Thermus Flavus

symmetry

Space Group: P -1

R_factor

R_Free

0.270

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
26.338	38.076	45.401	113.75	99.71	93.92

method

X-Ray Diffraction, 2 Models

resolution

1.40 Å

ligand

0C, 0G, 0U, CA

enzyme

Primary reference

The first crystal structure of an RNA racemate., Rypniewski W, Vallazza M, Perbandt M, Klussmann S, Delucas LJ, Betzel C, Erdmann VA, Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):659-64. Epub 2006, May 12. PMID:16699193

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]

Biological Unit Coordinates (2gpm.pdb1.gz) 11 Kb

Biological Unit Coordinates (2gpm.pdb2.gz) 10 Kb

LPC: Ligand-Protein Contacts for 2GPM

CSU: Contacts of Structural Units for 2GPM

Likely Quarternary Molecular Structure file(s) for 2GPM

Structure Factors (187 Kb)

Retrieve 2GPM in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2GPM from S2C, [Save to disk]

View 2GPM 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 2GPM

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 2GPM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2gpm] [2gpm_M] [2gpm_K] [2gpm_N] [2gpm_L]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 2GPM

Community annotation for 2GPM 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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