Research workbench
Crystal structure of the complex between CCL17 and M116 Fab
Analyse Crystal structure of the complex between CCL17 and M116 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WK3
- Type
- protein
- Length
- 2,002 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M116 light chain; M116 heavy chain; C-C motif chemokine 17
- UniProt
- Q92583
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, R | M116 light chain | protein | 217 | 7% helix, 51% strand | — |
| Q, S, U, W | M116 heavy chain | protein | 221 | 8% helix, 50% strand | — |
| T | M116 light chain | protein | 218 | 7% helix, 51% strand | — |
| V | M116 light chain | protein | 216 | 7% helix, 51% strand | — |
| A | C-C motif chemokine 17 | protein | 62 | 27% helix, 24% strand | Q92583 |
| B | C-C motif chemokine 17 | protein | 63 | 27% helix, 24% strand | Q92583 |
| C | C-C motif chemokine 17 | protein | 64 | 23% helix, 23% strand | Q92583 |
| D | C-C motif chemokine 17 | protein | 61 | 28% helix, 25% strand | Q92583 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains P, Q, R, S, T, U, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.73 | 0.77 | 84 | empty |
| 2 | 1127 | 0.71 | 0.75 | 107 | empty |
| 3 | 379 | 0.61 | 0.77 | 48 | empty |
| 4 | 373 | 0.55 | 0.74 | 45 | empty |
| 5 | 298 | 0.54 | 0.76 | 47 | empty |
Interfaces
22 interfaces between chains.
- V–W · 1805 Ų buried · 17 hydrogen bonds · protein-protein
- P–Q · 1781 Ų buried · 16 hydrogen bonds · protein-protein
- R–S · 1760 Ų buried · 15 hydrogen bonds · protein-protein
- T–U · 1755 Ų buried · 17 hydrogen bonds · protein-protein
- Q–C · 485 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5WK3 · Crystal structure of the complex between CCL17 and M116 Fab · the same entry in another collection · chain D against D, 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 Q92583
- Elsewhere: RCSB PDB 5WK3 · PDBe 5WK3 · UniProt Q92583
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