Research workbench
X-ray structure of macrophage inflammatory protein-1 alpha (CCL3) N- terminal-switch polymer
Analyse X-ray structure of macrophage inflammatory protein-1 alpha (CCL3) N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5COR
- Type
- protein
- Length
- 688 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C motif chemokine 3
- UniProt
- P10147
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, J | C-C motif chemokine 3 | protein | 70 | 20% helix, 26% strand | P10147 |
| B, D, E, H | C-C motif chemokine 3 | protein | 68 | 21% helix, 26% strand | P10147 |
| C | C-C motif chemokine 3 | protein | 67 | 22% helix, 27% strand | P10147 |
| I | C-C motif chemokine 3 | protein | 69 | 22% helix, 26% strand | P10147 |
Ligands and binding sites
- HEZ · Hexane-1,6-diol · additive · 10 copies · chains A, B, C, E, G, F, H, J
- ACT · Acetate ion · additive · 3 copies · chains F, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.78 | 0.83 | 85 | HEZ |
| 2 | 881 | 0.74 | 0.78 | 78 | HEZ |
| 3 | 173 | 0.68 | 0.87 | 32 | empty |
| 4 | 330 | 0.68 | 0.82 | 46 | ACT |
| 5 | 158 | 0.68 | 0.87 | 25 | empty |
Interfaces
17 interfaces between chains.
- G–H · 752 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 750 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 740 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 721 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 691 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5COR · X-ray structure of macrophage inflammatory protein-1 alpha (CCL3) N-terminal-switch… · the same entry in another collection · chain J against J, TM-score 1.00
- P10147 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 3 (P10147) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P10147
- Elsewhere: RCSB PDB 5COR · PDBe 5COR · UniProt P10147
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