OCA Atlas for 1OQS

1OQS

Hydrolase

date

Mar 11, 2003

title

Crystal Structure Of Rv4rv7 Complex

authors

M.Perbandt, C.Betzel

compound

source

Molecule: Phospholipase A2 Rv-7
Chain: A, C, E, G
Synonym: Phosphatidylcholine 2-Acylhydrolase, Phospholipase A2 Inhibitor;
Ec: 3.1.1.4

Organism_scientific: Daboia Russellii Siamensis
Organism_taxid: 343250
Strain: Siamensis
Secretion: Venom

Molecule: Phospholipase A2 Rv-4
Chain: B, D, F, H
Synonym: Phosphatidylcholine 2-Acylhydrolase
Ec: 3.1.1.4

Organism_scientific: Daboia Russellii Siamensis
Organism_taxid: 343250
Strain: Siamensis
Secretion: Venom

symmetry

Space Group: P 1 21 1

R_factor

0.222

R_Free

0.284

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
74.918	85.125	78.159	90.00	95.10	90.00

method

X-Ray Diffraction

resolution

1.90 Å

ligand

enzyme

Hydrolase E.C.3.1.1.4 BRENDA

related structures

by homologous chain: 1AOK, 1Q5T

Gene
Ontology

Chain	Function	Process	Component
A, E, C, G	phospholipase A2 inhibitor a... toxin activity
F, B, H, D	toxin activity

Primary reference

Structure of the heterodimeric neurotoxic complex viperotoxin F (RV-4/RV-7) from the venom of Vipera russelli formosensis at 1.9 A resolution., Perbandt M, Tsai IH, Fuchs A, Banumathi S, Rajashankar KR, Georgieva D, Kalkura N, Singh TP, Genov N, Betzel C, Acta Crystallogr D Biol Crystallogr 2003 Oct;59(Pt 10):1679-87. PMID:14501106

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (167 Kb) [Save to disk]

Biological Unit Coordinates (1oqs.pdb1.gz) 43 Kb

Biological Unit Coordinates (1oqs.pdb2.gz) 42 Kb

Biological Unit Coordinates (1oqs.pdb3.gz) 42 Kb

Biological Unit Coordinates (1oqs.pdb4.gz) 43 Kb

CSU: Contacts of Structural Units for 1OQS

Likely Quarternary Molecular Structure file(s) for 1OQS

Structure Factors (1121 Kb)

Retrieve 1OQS in mmCIF format [Save to disk]

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

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

View 1OQS 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 1OQS

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 1OQS, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1oqsa_, region A [Jmol] [rasmolscript] [script source]
- Domain d1oqsb_, region B [Jmol] [rasmolscript] [script source]
- Domain d1oqsc_, region C [Jmol] [rasmolscript] [script source]
- Domain d1oqsd_, region D [Jmol] [rasmolscript] [script source]
- Domain d1oqse_, region E [Jmol] [rasmolscript] [script source]
- Domain d1oqsf_, region F [Jmol] [rasmolscript] [script source]
- Domain d1oqsg_, region G [Jmol] [rasmolscript] [script source]
- Domain d1oqsh_, region H [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: [1oqs_E] [1oqs] [1oqs_F] [1oqs_B] [1oqs_A] [1oqs_C] [1oqs_D] [1oqs_G] [1oqs_H]

SWISS-PROT database: [Q02471] [P31100]

Domain organization of [PA24_DABRU] [PA27_DABRU] by SWISSPFAM

Domain found in 1OQS: [PA2c ] by SMART

Other resources with information on 1OQS

Community annotation for 1OQS 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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