MSDlite | EMBL-EBI
Simple search interface to the Macromolecular Structure Database.

Structure Group@NCBI
Entrez search of the databases supported by the NCBI Structure Group:

1. MMDB: a database of macromolecular 3D structures, that contains experimentally determined biopolymer structures obtained from the Protein Data Bank (PDB)
2. PubVast: a database of structure-structure alignments. Each protein chain and 3D domain from MMDB is compared with all the others using the VAST (Vector Alignment Search Tool) algorithm
3. PubChem: a database of small molecules, which provides information on their biological activities
4. CDD: the Conserved Domain Database consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. These are available as position-specific score matrices (PSSMs), for the rapid identification of conserved domains in protein sequences

PDBsum | EMBL-EBI
PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.