MolNFT v1 · #103655 · protein
Structure of the cytomegalovirus-encoded M04 glycoprotein
4PN6: “Structure of the cytomegalovirus-encoded M04 glycoprotein”. X-ray diffraction, 2 ligands (NAG, MAN), 4 pockets (best druggability 0.64). MolNFT v1 #103655 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PN6
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M04
- UniProt
- B3UWV7
- Ligands
- NAG, MAN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M04 | protein | 167 | 10% helix, 40% strand | B3UWV7 |
| B | M04 | protein | 168 | 8% helix, 39% strand | B3UWV7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
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 | 516 | 0.64 | 0.76 | 46 | empty |
| 2 | 194 | 0.48 | 0.76 | 29 | empty |
| 3 | 97 | 0.42 | 0.78 | 18 | empty |
| 4 | 61 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1000 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 4PN6 · Structure of the Cytomegalovirus-Encoded m04 Glycoprotein · 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 B3UWV7
- Elsewhere: RCSB PDB 4PN6 · PDBe 4PN6 · UniProt B3UWV7
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