MolNFT v1 · #113424 · protein
Mael domain from bombyx mori maelstrom
5AF0: “Mael domain from bombyx mori maelstrom”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.72). MolNFT v1 #113424 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AF0
- Type
- protein
- Length
- 950 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maelstrom
- UniProt
- H9JFX7
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maelstrom | protein | 237 | 43% helix, 18% strand | H9JFX7 |
| B | Maelstrom | protein | 236 | 45% helix, 19% strand | H9JFX7 |
| C | Maelstrom | protein | 239 | 42% helix, 18% strand | H9JFX7 |
| D | Maelstrom | protein | 238 | 42% helix, 18% strand | H9JFX7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.72 | 0.78 | 72 | empty |
| 2 | 425 | 0.66 | 0.79 | 54 | empty |
| 3 | 112 | 0.52 | 0.82 | 29 | empty |
| 4 | 149 | 0.52 | 0.79 | 21 | empty |
| 5 | 148 | 0.51 | 0.79 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 578 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 307 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 96 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5AF0 · MAEL domain from Bombyx mori Maelstrom · 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
- Every structure of UniProt H9JFX7
- Elsewhere: RCSB PDB 5AF0 · PDBe 5AF0 · UniProt H9JFX7
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