MolNFT v1 · #112452 · protein
Crystal structure of viral chemokine binding protein R17 in complex with CCL3
4ZLT · Putative uncharacterized protein: “Crystal structure of viral chemokine binding protein R17 in complex with CCL3”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.84). MolNFT v1 #112452 on GenesisL1: 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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