Research workbench
S100Z from zebrafish in complex with calcium
Analyse S100Z from zebrafish in complex with calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y5I
- Type
- protein
- Length
- 584 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S100 calcium binding protein Z
- UniProt
- Q503K9
- Ligands
- CA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S100 calcium binding protein Z | protein | 97 | 71% helix, 4% strand | Q503K9 |
| B | S100 calcium binding protein Z | protein | 96 | 72% helix, 4% strand | Q503K9 |
| C, D, F | S100 calcium binding protein Z | protein | 98 | 71% helix, 4% strand | Q503K9 |
| E | S100 calcium binding protein Z | protein | 97 | 71% helix, 4% strand | Q503K9 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
- IPA · Isopropyl alcohol · additive · 6 copies · chains A, C, E, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.70 | 0.85 | 33 | IPA |
| 2 | 244 | 0.68 | 0.84 | 31 | IPA |
| 3 | 174 | 0.65 | 0.85 | 27 | empty |
| 4 | 123 | 0.62 | 0.86 | 20 | empty |
| 5 | 74 | 0.59 | 0.88 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1599 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1559 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1553 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 979 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 951 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2Y5I · S100Z from zebrafish in complex with calcium · 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 Q503K9
- Elsewhere: RCSB PDB 2Y5I · PDBe 2Y5I · UniProt Q503K9
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