Research workbench
Convergent evolution involving dimeric and trimeric dutpases in signalling.
Analyse Convergent evolution involving dimeric and trimeric dutpases in signalling. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MYD
- Type
- protein
- Length
- 649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutpase
- EC
- 3.6.1.23
- Ligands
- DUP, MG
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dutpase (EC 3.6.1.23) | protein | 160 | 71% helix, 0% strand | — |
| B | Dutpase (EC 3.6.1.23) | protein | 163 | 72% helix, 0% strand | — |
| C | Dutpase (EC 3.6.1.23) | protein | 164 | 71% helix, 0% strand | — |
| D | Dutpase (EC 3.6.1.23) | protein | 162 | 72% helix, 0% strand | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.69 | 0.79 | 65 | empty |
| 2 | 365 | 0.63 | 0.79 | 37 | empty |
| 3 | 183 | 0.51 | 0.77 | 21 | empty |
| 4 | 134 | 0.43 | 0.76 | 21 | DUP |
| 5 | 89 | 0.42 | 0.78 | 19 | DUP |
Interfaces
5 interfaces between chains.
- C–D · 694 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 313 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 92 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 69 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5MYD · Convergent evolution involving dimeric and trimeric dUTPases in signalling. · 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 5MYD · PDBe 5MYD
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