MolNFT v1 · #124297 · protein
Structure of spelter bound to ZN2+
5KAY: “Structure of spelter bound to ZN2+”. X-ray diffraction, 2 ligands (ZN, NA), 7 pockets (best druggability 0.52). MolNFT v1 #124297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KAY
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spelter
- Ligands
- ZN, NA
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spelter | protein | 201 | 57% helix, 6% strand | — |
| B | Spelter | protein | 200 | 58% helix, 8% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.52 | 0.82 | 17 | empty |
| 2 | 137 | 0.51 | 0.80 | 17 | empty |
| 3 | 202 | 0.48 | 0.75 | 39 | empty |
| 4 | 59 | 0.44 | 0.83 | 18 | empty |
| 5 | 133 | 0.43 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 717 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5KAY · Structure of Spelter bound to Zn2+ · 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 5KAY · PDBe 5KAY
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