Research workbench
Crystal structure of human CALPROTECTIN(S100A8/S100A9)
Analyse Crystal structure of human CALPROTECTIN(S100A8/S100A9) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XK4
- Type
- protein
- Length
- 1,072 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calgranulin a; Calgranulin B
- UniProt
- P05109, P06702
- Ligands
- CA, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I | Calgranulin a | protein | 87 | 68% helix, 2% strand | P05109 |
| B, J | Calgranulin a | protein | 88 | 67% helix, 2% strand | P05109 |
| C, H | Calgranulin B | protein | 89 | 65% helix, 2% strand | P06702 |
| D, G, K, L | Calgranulin B | protein | 92 | 66% helix, 4% strand | P06702 |
| E | Calgranulin a | protein | 89 | 66% helix, 2% strand | P05109 |
Ligands and binding sites
- CA · Calcium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 4 copies · chains A, F, J
- FLC · Citrate anion · additive · chains F, H, J, L
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 | 763 | 0.78 | 0.82 | 74 | empty |
| 2 | 232 | 0.78 | 0.92 | 30 | FLC |
| 3 | 657 | 0.77 | 0.82 | 71 | empty |
| 4 | 602 | 0.76 | 0.82 | 63 | empty |
| 5 | 328 | 0.56 | 0.75 | 39 | empty |
Interfaces
22 interfaces between chains.
- I–K · 1508 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1481 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1460 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 1460 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1432 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1XK4 · Crystal structure of human calprotectin(S100A8/S100A9) · the same entry in another collection · chain L against L, 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 P05109
- Every structure of UniProt P06702
- Elsewhere: RCSB PDB 1XK4 · PDBe 1XK4 · UniProt P05109 · UniProt P06702
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