Research workbench
Crystal structure of viral chemokine binding protein R17 in complex with CCL3
Analyse Crystal structure of viral chemokine binding protein R17 in complex with CCL3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZLT
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; C-C motif chemokine 3
- UniProt
- E9M5R0, P10855
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Putative uncharacterized protein | protein | 379 | 6% helix, 49% strand | E9M5R0 |
| A | Putative uncharacterized protein | protein | 376 | 7% helix, 48% strand | E9M5R0 |
| F, L | C-C motif chemokine 3 | protein | 62 | 23% helix, 35% strand | P10855 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.84 | 0.89 | 81 | empty |
| 2 | 1051 | 0.84 | 0.85 | 107 | empty |
| 3 | 256 | 0.77 | 0.90 | 44 | empty |
| 4 | 86 | 0.56 | 0.86 | 19 | empty |
| 5 | 176 | 0.52 | 0.79 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–L · 1494 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1400 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 929 Ų buried · 9 hydrogen bonds · protein-protein
- B–L · 685 Ų buried · 12 hydrogen bonds · protein-protein
- F–L · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4ZLT · Crystal structure of viral chemokine binding protein R17 in complex with CCL3 · the same entry in another collection · chain B against B, TM-score 1.00
- P10855 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 3 (P10855) · a predicted model of the same protein · chain L against A, TM-score 0.93
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 E9M5R0
- Every structure of UniProt P10855
- Elsewhere: RCSB PDB 4ZLT · PDBe 4ZLT · UniProt E9M5R0 · UniProt P10855
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