Table 1.
PDB entries including POMs modeled by the authors.
| PDB entry | Protein name (organism) | POM sum formula | ID | Origin of POM | Purpose of POM use | POM impact on crystallization/structure | Ref. |
|---|---|---|---|---|---|---|---|
| 1L7V | ABC transporter (E. coli) | [V4O12]4− | V4O | Self-assembly in the presence of VO43− (inhibitor) | Heavy atom derivative for phasing | Providing initial phases | [94] |
| 2D1G | Acid Phosphatase A (F. tularensis) | [V10O28]6− | DVT | Self-assembly in the presence of Na3VO4 (inhibitor) | None | Structure stabilization (POM rigidifies a flexible His6-tag) | [81] |
| 1UZI | C3 exoenzyme (C. botulinum) | [V4O12]4− | V4O | Self-assembly in the presence of Na3VO4 | None | Involvement in crystal packing | [85] |
| 1E59 | Cofactor-dependent phosphoglycerate mutase (E. coli) | [V4O13]6− | VO3 | Self-assembly in the presence of NaVO3 (inhibitor) | NaVO3 as mutase inhibitor | Inhibition, stabilization of the inactive form | [95] |
| 3GQI | Human activated receptor tyrosine kinase | [V10O28]6− | DVT | Self-assembly in the presence of Na3VO4 (inhibitor) | None | Structure stabilization | [80] |
| 1DKT | Human cell cycle protein CksHs1 | [V7O19]3− | V7O | Self-assembly in the presence of VO3− (phosphate analog) | Substrate analog | Binding to active site, stabilization of the protein's dimer | [96] |
| 2HHL | Human CTD small phosphatase-like protein | [PW12O40]3− | KEG | Not described in reference | Not described | Possible involvement in crystal packing | [78] |
| 1N7D | Human extracellular domain of the LDL-receptor | [PW12O40]3− | KEG | Soaking in Na3[PW12O40] | Anomalous scatterer for phasing | Crystal quality improvement by stabilization of domain packing, providing initial phases | [76] |
| 4OUA | Latent and active mushroom tyrosinase PPO4 (A. bisporus) | [TeW6O24]6− | TEW | Co-crystallization with Na6[TeW6O24] | Crystallization additive | Involvement in crystal packing (no crystal without POM) | [14] |
| 4PHI | Lysozyme (G. gallus) | [TeW6O24]6− | TEW | Co-crystallization with Na6[TeW6O24] | Crystallization additive | Involvement in crystal packing, induction of new crystal form | [15] |
| 4B1A | Lysozyme (G. gallus) | [PMo12O40]3− | K3G | Byproduct of pro-drug decomposition | None | Structure stabilization | [90] |
| 4F6T | Molybdenum storage protein (A. vinelandii) | [Mo6O26]16− | 6M0 | Protein induced assembly in the presence of Na2MoO4 | Analysis of the assembled POMs | POMs are formed and stabilized by the protein matrix | [51] |
| 4F6T | Molybdenum storage protein (A. vinelandii) | [Mo8O28]8− | 8M0 | Protein induced assembly in the presence of Na2MoO4 | Analysis of the assembled POMs | POMs are formed and stabilized by the protein matrix | [51] |
| 2OGX | Molybdenum storage protein (A. vinelandii) | [W3O13]8− | WO3 | Protein induced assembly in the presence of WO42− | Analysis of the assembled POMs | POMs are formed and stabilized by the protein matrix | [50] |
| 4NDOa | Molybdenum storage protein (A. vinelandii) | [Mo3O13]8− | M10 | Protein induced assembly in the presence of Na2MoO4 | Analysis of the assembled POMs | POMs are formed and stabilized by the protein matrix | [52] |
| 4NDOa | Molybdenum storage protein (A. vinelandii) | [Mo8O28]8− | 8M0 | Protein induced assembly in the presence of Na2MoO4 | Analysis of the assembled POMs | POMs are formed and stabilized by the protein matrix | [52] |
| 4BVO | NTPDase1 (L. pneumophila) | [W12O40H2]6− | E43 | Co-crystallization with Na6[W12O40H2] | As inhibitor | Induction of new crystal form (partially opened active site) | [53] |
| 4BVP | NTPDase1 (L. pneumophila) | [Mo8O28]8− | 8M0 | Soaking in (NH4)6[Mo7O24] | Hydrolase inhibitor | Involvement in crystal packing (rigidifying a flexible His6-tag) | [53] |
| 4BVP | NTPDase1 (L. pneumophila) | [Mo7O24]6− | MO7 | Soaking in (NH4)6[Mo7O24] | Hydrolase inhibitor | Rigidifying flexible protein regions | [53] |
| 4BVP | NTPDase1 (L. pneumophila) | [Mo3O14]10− | 6LL | Degradation product of (NH4)6[Mo7O24] | Hydrolase inhibitor | Rigidifying flexible protein regions | [53] |
| 4BRH | NTPDase1 (L. pneumophila) | [V10O28]6− | DVT | Self-assembly in the presence of VO43− (phosphate mimic) | None | No special impact | [79] |
| 3ZX0 | NTPDase1 (R. norvegicus) | [Mo7O24]6− | MO7 | Soaking in (NH4)6[Mo7O24] | Hydrolase inhibitor | Inhibition and conformation stabilization | [97] |
| 3ZX2 | NTPDase1 (R. norvegicus) | [V10O28]6− | DVT | Self-assembly upon soaking in Na3VO4 | Hydrolase inhibitor | Inhibition and conformation stabilization | [97] |
| 1P0Z | Sensor kinase CitA (K. pneumonia) | [Mo7O24]6− | MO7 | Self-assembly in the presence of Na2MoO4 (inhibitor) | None | Involvement in crystal packing | [77] |
| 1I94b | Small ribosomal subunit (T. thermophilus) | [P2W18O62]6− | WO2 | Soaking in K6[P2W18O62] (additive) | Phasing and rigidifying | Increase in resolution by rigidifying flexible protein regions | [91] |
| 1FKA | Small ribosomal subunit (T. thermophilus) | [P2W18O62]6− | WO2 | Soaking in K6[P2W18O62] (additive) | Phasing and rigidifying | Increase in resolution by rigidifying flexible protein regions | [11] |
| 1DV4 | Small ribosomal subunit (T. thermophilus) | [P2W18O62]6− | WO2 | Soaking in K6[P2W18O62] (additive) | Phasing and rigidifying | Increase in resolution by rigidifying flexible protein regions | [10] |
| 1RXS | Uridine Phosphorylase (E. coli) | [V7O19]3− | V7O | Self-assembly in the presence of NaVO3 (buffer component) | None | None | [98] |
a
PDB entries 4NDP, 4NDQ and 4NDR contain the same POM exhibiting the same effect and are therefore not listed.
b
PDB entries 1I95–1I97 contain the same POM exhibiting the same effect and are therefore not listed.