MolNFT v1 · #102331 · protein
X-ray crystal structure of racemic non-glycosylated chemokine ser-CCL1
4OIJ · C-C motif chemokine 1: “X-ray crystal structure of racemic non-glycosylated chemokine ser-CCL1”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.51). MolNFT v1 #102331 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4OIJ
- Type
- protein
- Length
- 278 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C motif chemokine 1; D-ser-CCL1
- UniProt
- P22362
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-C motif chemokine 1 | protein | 71 | 20% helix, 32% strand | P22362 |
| C, D | D-ser-CCL1 | protein | 68 | 21% helix, 31% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 31 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.51 | 0.74 | 33 | SO4 |
| 2 | 133 | 0.42 | 0.75 | 24 | empty |
| 3 | 97 | 0.31 | 0.72 | 17 | SO4 |
| 4 | 69 | 0.29 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1144 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 816 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 193 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 143 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 130 d-amino, 12 disulfide (D-amino acid, disulfide).
Compared structures
- 4OIJ · X-ray crystal structure of racemic non-glycosylated chemokine Ser-CCL1 · the same entry in another collection · chain A against A, TM-score 1.00
- P22362 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 1 (P22362) · a predicted model of the same protein · chain B 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 P22362
- Elsewhere: RCSB PDB 4OIJ · PDBe 4OIJ · UniProt P22362
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