Research workbench
Evolutionary history and metabolic insights of ancient mammalian uricases
Analyse Evolutionary history and metabolic insights of ancient mammalian uricases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MB8
- Type
- protein
- Length
- 1,146 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uricase
- EC
- 1.7.3.3
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uricase (EC 1.7.3.3) | protein | 285 | 24% helix, 43% strand | — |
| B | Uricase (EC 1.7.3.3) | protein | 286 | 24% helix, 43% strand | — |
| C | Uricase (EC 1.7.3.3) | protein | 285 | 24% helix, 43% strand | — |
| D | Uricase (EC 1.7.3.3) | protein | 290 | 23% helix, 43% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.80 | 0.81 | 102 | ACT |
| 2 | 1084 | 0.78 | 0.80 | 101 | empty |
| 3 | 747 | 0.69 | 0.76 | 72 | empty |
| 4 | 713 | 0.68 | 0.76 | 66 | empty |
| 5 | 261 | 0.53 | 0.75 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3166 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 3123 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 2933 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 2916 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 370 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4MB8 · Evolutionary history and metabolic insights of ancient mammalian uricases · 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 4MB8 · PDBe 4MB8
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