The 3D-GENOMICS database provides structural annotations for proteins from sequenced genomes.
http://www.sbg.bio.ic.ac.uk/3dgenomics/

ArchDB contains an automated classification of protein loop structure.
http://sbi.imim.es/cgi-bin/archdb/loops.pl

The ASTRAL compendium provides databases and tools useful for analyzing protein structures and their sequences.
http://astral.berkeley.edu/

BAliBASE is a database for the comparison of multiple sequence alignments.
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html

BMRB is a repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids.
http://www.bmrb.wisc.edu/

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank.
http://cluster.physics.iisc.ernet.in/cadb/

CATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
http://www.biochem.ucl.ac.uk/bsm/cath_new/

The CE-Database provides databases and tools for 3D protein structure comparison and alignment using the Combinatorial Extension (CE) Method.
http://cl.sdsc.edu/ce.html

The world repository of small molecule crystal structures.
http://www.ccdc.cam.ac.uk/products/csd/

Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
http://divac.ist.temple.edu/disprot/

DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.
http://caps.ncbs.res.in/dsdbase/dsdbase.html

The E-MSD macromolecular structure relational database is designed to be a single access point for protein and nucleic acid structures and related information.
http://www.ebi.ac.uk/msd/index.html

eFsite (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms.
http://ef-site.protein.osaka-u.ac.jp/eF-site/

Genomic Distribution of Structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. The database has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases.
http://caps.ncbs.res.in/gendis/home.html

The Genomic Threading Database (GTD) contains structural annotations of proteomes, translated from the genomes of key organisms.
http://bioinfadmin.cs.ucl.ac.uk/GTD/

GTOP is a database built by the Laboratory of Gene-product Informatics at the National Institute of Genetics consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures. This research is supported by the Japan Science and Technology Corporation and Grants-in-Aid for Scientific Research (Genomes in category C) from the Ministry of Education, Science, Sports and Culture of Japan.
http://spock.genes.nig.ac.jp/~genome/

Proteins in Protein DataBank contains a lot of hetero atoms (Atoms that compose non-protein molecules). This information is useful to analyze protein-ligand/protein-substrate interactions. In Het-PDB Navi, information for hetero atoms is obtained through PDB ID and hetero atom name.
http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html

HIC-Up is a server for hetero-compounds ("small molecules").
http://xray.bmc.uu.se/hicup/

The IMB Jena Image Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.
http://www.imb-jena.de/IMAGE.html

IMGT/3Dstructure-DB and IMGT/Structural-Query are a 3D structure database and a tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools.
http://imgt3d.igh.cnrs.fr

KEGG LIGAND Database. The universe of chemical reactions involving metabolites and other biochemical compounds, as well as xenobiotic compounds.
http://www.genome.ad.jp/ligand/

NCBI's Entrez includes a database of experimentally determined three-dimensional biomolecular structures. Most 3D structure data are obtained from X-ray crystallography and NMR spectroscopy; they provide a wealth of information on biological function, on mechanisms linked to the function, and on the evolutionary history of and relationships between macromolecules.
http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

MODBASE is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure.
http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi

The Database of Macromolecular Movements with Associated Tools for Geometric Analysis describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.
http://molmovdb.mbb.yale.edu/molmovdb/

PASS2 is a database of structural motifs of protein superfamilies.
http://caps.ncbs.res.in/campass/pass.html

PepConf is a database of peptide conformations.
http://www.peptidome.org/products/list.htm

The Protein Folding Database (PFD) is a collection of all biophysical data relating to experimental protein folding studies.
The database contains structural, methodological, kinetic and thermodynamic data, and contains data for 52 proteins, representing 39 SCOP families, and 18 organisms.
http://pfd.med.monash.edu.au

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships.
http://scop.mrc-lmb.cam.ac.uk/scop/

The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function.
http://ssd.rbvi.ucsf.edu/

The SURFACE database is a repository of annotated and compared protein surface regions.
http://cbm.bio.uniroma2.it/surface/

The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. The repository is developed at the Biozentrum Basel within the Swiss Institute of Bioinformatics.
http://swissmodel.expasy.org/repository/

TargetDB is a target registration database funded by the NIH that was developed to provide registration and tracking information for the NIH P50 structural genomics centers.
The scope of TargetDB is to provide timely status and tracking information on the progress of the production and solution of structures.
http://targetdb.pdb.org/

The TOPS database holds topological descriptions of protein structures.
http://www.tops.leeds.ac.uk