OCA Atlas for 1LB2

1LB2

Gene Regulation Dna

date

Apr 01, 2002

title

Structure Of The E. Coli Alpha C-Terminal Domain Of Rna Poly Complex With Cap And Dna

authors

B.Benoff, H.Yang, C.L.Lawson, G.Parkinson, J.Liu, E.Blatter, Y.W.E H.M.Berman, R.H.Ebright

compound

source

Molecule: 5'-D(Cptptptptptptpcpcptpapapapapt Apt)-3';
Chain: K
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Cptpapgpaptpcpapcpaptptptptpa Apapapapapg)-3';
Chain: J
Engineered: Yes

Synthetic: Yes

Molecule: Catabolite Gene Activator Protein
Chain: A
Synonym: Cap, Camp Receptor Protein, Camp-Regulatory Protei
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase Alpha Chain
Chain: B, E
Fragment: Alpha Ctd, Alpha Carboxy Terminal Domain
Synonym: Transcriptase Alpha Chain, Rna Polymerase Alpha Su
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

symmetry

Space Group: P 62 2 2

R_factor

0.211

R_Free

0.244

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
175.970	175.970	158.020	90.00	90.00	120.00

method

X-Ray Diffraction

resolution

3.10 Å

ligand

CMP BindingDB

enzyme

Transferase E.C.2.7.7.6 BRENDA

note

1LB2 (Molecule of the Month:pdb48)

Gene
Ontology

Chain	Function	Process	Component
A
E, B

Primary reference

Structural basis of transcription activation: the CAP-alpha CTD-DNA complex., Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH, Science 2002 Aug 30;297(5586):1562-6. PMID:12202833

Data retrieval

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

Biological Unit Coordinates (1lb2.pdb1.gz) 132 Kb

LPC: Ligand-Protein Contacts for 1LB2

CSU: Contacts of Structural Units for 1LB2

Likely Quarternary Molecular Structure file(s) for 1LB2

Structure Factors (267 Kb)

Retrieve 1LB2 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1LB2 from S2C, [Save to disk]

Re-refined 1lb2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1LB2 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 1LB2

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 1LB2, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1lb2a1, region A:138-209 [Jmol] [rasmolscript] [script source]
- Domain d1lb2a2, region A:9-137 [Jmol] [rasmolscript] [script source]
- Domain d1lb2b_, region B [Jmol] [rasmolscript] [script source]
- Domain d1w1lb2, region B:6-273 [Jmol] [rasmolscript] [script source]
- Domain d1lb2e_, region E [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: [1lb2] [1lb2_B] [1lb2_K] [1lb2_J] [1lb2_E] [1lb2_A]

SWISS-PROT database: [P0ACJ8] [P0A7Z4]

Domain organization of [CRP_ECOLI] [RPOA_ECOLI] by SWISSPFAM

Domains found in 1LB2: [HTH_CRP] [cNMP ] by SMART

Other resources with information on 1LB2

Community annotation for 1LB2 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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