MolNFT v1 · #138183 · protein
US28 bound to engineered chemokine CX3CL1.35 and nanobodies
5WB2 · Envelope protein US28, nanobody 7 fusion protein: “US28 bound to engineered chemokine CX3CL1.35 and nanobodies”. X-ray diffraction, 2 ligands (CLR, ZN), 7 pockets (best druggability 0.71). MolNFT v1 #138183 on GenesisL1: 3D…
- PDB
- 5WB2
- Type
- protein
- Length
- 621 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein US28, nanobody 7 fusion protein; CX3CL1 protein; Nanobody B1
- UniProt
- Q80KM9, Q6I9S9
- Ligands
- CLR, ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein US28, nanobody 7 fusion protein | protein | 421 | 54% helix, 19% strand | Q80KM9 |
| B | CX3CL1 protein | protein | 73 | 19% helix, 23% strand | Q6I9S9 |
| D | Nanobody B1 | protein | 127 | 5% helix, 46% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.71 | 0.94 | 26 | MES |
| 2 | 343 | 0.67 | 0.81 | 36 | empty |
| 3 | 306 | 0.58 | 0.77 | 28 | empty |
| 4 | 83 | 0.51 | 0.84 | 18 | empty |
| 5 | 86 | 0.42 | 0.78 | 14 | OLC |
Interfaces
2 interfaces between chains.
- A–B · 1592 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 927 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 modified (disulfide, alkylation, cyclization).
Compared structures
- 5WB2 · US28 bound to engineered chemokine CX3CL1.35 and nanobodies · the same entry in another collection · chain A against A, 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 Q80KM9
- Every structure of UniProt Q6I9S9
- Elsewhere: RCSB PDB 5WB2 · PDBe 5WB2 · UniProt Q80KM9 · UniProt Q6I9S9
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