Research workbench
Crystal structure of NI(II)- and CA(II)-bound human calprotectin
Analyse Crystal structure of NI(II)- and CA(II)-bound human calprotectin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W1F
- Type
- protein
- Length
- 779 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein S100-A8; Protein S100-A9
- UniProt
- P05109, P06702
- Ligands
- CA, NA, NI
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein S100-A8 | protein | 87 | 67% helix, 2% strand | P05109 |
| B, H | Protein S100-A9 | protein | 107 | 58% helix, 2% strand | P06702 |
| C, G, E | Protein S100-A8 | protein | 88 | 67% helix, 5% strand | P05109 |
| D | Protein S100-A9 | protein | 108 | 56% helix, 2% strand | P06702 |
| F | Protein S100-A9 | protein | 106 | 58% helix, 2% strand | P06702 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, G, H, E, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, G, H, E
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, G, H, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.83 | 0.84 | 83 | empty |
| 2 | 245 | 0.83 | 0.95 | 23 | empty |
| 3 | 798 | 0.77 | 0.81 | 60 | empty |
| 4 | 459 | 0.66 | 0.78 | 47 | empty |
| 5 | 326 | 0.59 | 0.77 | 34 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1636 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1633 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1593 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 523 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5W1F · Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin · the same entry in another collection · chain F against F, TM-score 1.00
- P06702 · AlphaFold monomer V2.0 prediction for protein S100-A9 (P06702) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 5W1F · PDBe 5W1F · UniProt P05109 · UniProt P06702
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