1D5D	Hydrolase	date	Oct 07, 1999
title	The Role Of Phenylalanine 8 In The Stabilization Of The S Pr Peptide Interaction: Packing And Cavities
authors	G.S.Ratnaparkhi, R.Varadarajan
compound		source
Molecule: S Peptide Chain: A Fragment: Residues 1-15 Engineered: Yes Mutation: Yes Other_details: Synthetic		Synthetic: Yes Other_details: S15 Peptide Synthesized By Solid Phase Pepti Synthesis;
Molecule: Rnase S Chain: B Fragment: Residues 21-124		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Other_details: Derieved From A Limit Digest Of Bovine Pancr Rnase A
symmetry	Space Group: P 31 2 1	R_factor 0.189 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.840 44.840 98.000 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.25 Å
ligand	SET, SO4	enzyme
related structures	by homologous chain: 1FEV, 1R3M
Gene Ontology	Chain Function Process Component B
Primary reference	Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics., Ratnaparkhi GS, Varadarajan R, Biochemistry 2000 Oct 10;39(40):12365-74. PMID:11015216

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk] Biological Unit Coordinates (1d5d.pdb1.gz) 26 Kb LPC: Ligand-Protein Contacts for 1D5D CSU: Contacts of Structural Units for 1D5D Likely Quarternary Molecular Structure file(s) for 1D5D Structure Factors (40 Kb) Retrieve 1D5D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D5D from S2C, [Save to disk] Re-refined 1d5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1D5D 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 1D5D

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 1D5D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d5d.1, region A:,B [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: [1d5d] [1d5d_B] [1d5d_A] SWISS-PROT database: [P61823] Domain organization of [RNAS1_BOVIN] by SWISSPFAM Domain found in 1D5D: [RNAse_Pc ] by SMART

Other resources with information on 1D5D

Community annotation for 1D5D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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