Research workbench
Crystal structure of MN2+ bound calprotectin
Analyse Crystal structure of MN2+ bound calprotectin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GGF
- Type
- protein
- Length
- 789 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, MN, SO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, S | Protein S100-A8 | protein | 89 | 66% helix, 2% strand | P05109 |
| C | Protein S100-A9 | protein | 108 | 57% helix, 2% strand | P06702 |
| L, T, V | Protein S100-A9 | protein | 109 | 57% helix, 2% strand | P06702 |
| U | Protein S100-A8 | protein | 87 | 67% helix, 2% strand | P05109 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, C, K, L, S, V, T, U
- MN · Manganese (II) ion · metal · 7 copies · chains A, C, K, L, S, T, U, V
- SO4 · Sulfate ion · ion · 3 copies · chains K, L, V
- GOL · Glycerol · additive · 6 copies · chains A, C, L, K, S, T, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.83 | 0.83 | 78 | GOL |
| 2 | 217 | 0.82 | 0.95 | 22 | empty |
| 3 | 687 | 0.78 | 0.83 | 52 | GOL |
| 4 | 521 | 0.63 | 0.76 | 62 | GOL |
| 5 | 189 | 0.48 | 0.75 | 35 | empty |
Interfaces
15 interfaces between chains.
- U–V · 1637 Ų buried · 22 hydrogen bonds · protein-protein
- S–T · 1636 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 1621 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1608 Ų buried · 22 hydrogen bonds · protein-protein
- T–V · 667 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4GGF · Crystal structure of Mn2+ bound calprotectin · the same entry in another collection · chain V against V, TM-score 1.00
- P06702 · AlphaFold monomer V2.0 prediction for protein S100-A9 (P06702) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P05109 · AlphaFold monomer V2.0 prediction for protein S100-A8 (P05109) · a predicted model of the same protein · chain U against A, TM-score 0.92
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 4GGF · PDBe 4GGF · UniProt P05109 · UniProt P06702
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