Table 2. Input structures and accessory data.
PDB | Chains | Res. (Å) | Dimer type | SASA (Å2) | Anchor | Chain | Loop | Loop length |
1dle | A/B | 2.1 | crystal dimer** | 2,800 | 38 | B | 36–40*** | 8 |
1fc4 | A/B | 2 | homodimer | 10,000 | 74 | B | 69–79 | 11 |
1qni | A/B | 2.4 | homodimer | 11,800 | 408 | B | 397–411 | 15 |
2qpv | A/B | 2.35 | homodimer | 2,900 | 55 | B | 50–57 | 8 |
3dxv | A/B | 2.21 | homodimer | 7,900 | 291 | B | 288–299 | 12 |
1u6e | A/B | 1.85 | homodimer | 6,700 | 86 | B | 80–89 | 10 |
2bwn | A/B | 2.1 | homodimer | 8,500 | 85 | B | 77–90 | 14 |
1jtp | M/B | 1.9 | heterodimer | 1,600 | 104 | B | 99–108 | 10 |
2hp2 | A/B | 2.7 | homodimer | 9,500 | 2306 | B | 2294–2309 | 16 |
2wya | B/C | 1.7 | homodimer | 5,900 | 1009 | C | 1003–1012 | 10 |
2obg | A* | 2.35 | heterodimer | 1,600 | 1080 | A | 1077–1086 | 10 |
2i25 | M/O | 1.8 | heterodimer | 1,400 | 91 | O | 86–93 | 8 |
3cgc | A/B | 2.3 | homodimer | 5,400 | 429 | B | 421–434 | 14 |
3ean | A/B | 2.75 | homodimer | 7,900 | 473 | B | 467–474 | 8 |
1fec | A/B | 1.7 | homodimer | 6,400 | 459 | B | 456–463 | 8 |
1zr0 | A/B | 1.8 | heterodimer | 1,400 | 15 | B | 10–17 | 8 |
This table collects structural parameters for the complexes used in this work, along with chosen parameters like anchor placement. The PDB column identifies the structure. The chains column identifies which complex within the PDB file was used (several have many complexes in the asymmetric unit). *: 2obg was not crystallized as a heterodimer; it was expressed as a fusion protein and crystallized as an infinitely domain-swapped polymer.[24] The resolution column contains the reported crystal structure resolution; all are reasonable. The dimer type column identifies the type of dimer. **: 1dle represents a crystal dimer rather than a biological one, making it a good test of weak interactions. The SASA column notes the area buried by the interface. The anchor and chain columns together identify the residue used as an anchor. The loop column identifies which residues (on the same chain as the anchor) were flexible. The loop length column collects the lengths of these loops. ***: 1dle has residues with insertion codes in the loops, leading to a longer loop than is obvious. The name column identifies the name and function of the protein as listed in the PDB.