Research workbench
Crystal structure of calcium and zinc-bound human S100A8 in space group P212121
Analyse Crystal structure of calcium and zinc-bound human S100A8 in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HLV
- Type
- protein
- Length
- 710 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein S100-A8
- UniProt
- P05109
- Ligands
- CA, ZN, CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, H | Protein S100-A8 | protein | 89 | 66% helix, 2% strand | P05109 |
| C | Protein S100-A8 | protein | 88 | 67% helix, 2% strand | P05109 |
| E, F | Protein S100-A8 | protein | 88 | 67% helix, 2% strand | P05109 |
| G | Protein S100-A8 | protein | 90 | 66% helix, 2% strand | P05109 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, D, B, H, C, E, F, G
- CL · Chloride ion · ion · 2 copies · chains F, G, B, H
- ACT · Acetate ion · additive · 6 copies · chains A, C, E, B, F, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.85 | 0.86 | 84 | ACT |
| 2 | 602 | 0.84 | 0.89 | 74 | ACT, CL |
| 3 | 318 | 0.58 | 0.77 | 42 | empty |
| 4 | 110 | 0.39 | 0.75 | 20 | empty |
| 5 | 55 | 0.32 | 0.76 | 13 | empty |
Interfaces
18 interfaces between chains.
- B–H · 1405 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1394 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1341 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1290 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 449 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5HLV · Crystal structure of calcium and zinc-bound human S100A8 in space group P212121 · the same entry in another collection · chain H against H, TM-score 1.00
- P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 P05109
- Elsewhere: RCSB PDB 5HLV · PDBe 5HLV · UniProt P05109
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