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Cyanophage S-2L mazg-like pyrophosphohydrolase bound to dgdp and three catalytic MN2+ ions per active site
Analyse Cyanophage S-2L mazg-like pyrophosphohydrolase bound to dgdp and three… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODY
- Type
- protein
- Length
- 385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mazg-like pyrophosphohydrolase (mazz)
- Ligands
- DGI, MN, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mazg-like pyrophosphohydrolase (mazz) | protein | 99 | 64% helix, 7% strand | — |
| B | Mazg-like pyrophosphohydrolase (mazz) | protein | 94 | 67% helix, 7% strand | — |
| C | Mazg-like pyrophosphohydrolase (mazz) | protein | 100 | 61% helix, 9% strand | — |
| D | Mazg-like pyrophosphohydrolase (mazz) | protein | 92 | 68% helix, 10% strand | — |
Ligands and binding sites
- DGI · 2'-deoxyguanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.78 | 0.84 | 71 | SO4, DGI, MN |
| 2 | 322 | 0.70 | 0.83 | 48 | DGI, MN, SO4 |
| 3 | 309 | 0.69 | 0.83 | 50 | SO4, DGI, MN |
| 4 | 201 | 0.45 | 0.74 | 41 | SO4 |
| 5 | 75 | 0.29 | 0.73 | 21 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 2714 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2610 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 463 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 299 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7ODY · Cyanophage S-2L MazG-like pyrophosphohydrolase bound to dGDP and three catalytic Mn2+… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7ODY · PDBe 7ODY
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