MolNFT v1 · #134901 · protein
The structure of the major capsid protein of pbcv-1
5TIP: “The structure of the major capsid protein of pbcv-1”. X-ray diffraction, 9 ligands (XXR, RM4, 7CV), 20 pockets (best druggability 0.82). MolNFT v1 #134901 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TIP
- Type
- protein
- Length
- 1,744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P30328
- Ligands
- XXR, RM4, 7CV, XYP, BGC, FUC, GLA, MAN, HG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Major capsid protein | protein | 436 | 20% helix, 35% strand | P30328 |
Ligands and binding sites
- XXR · alpha-D-rhamnopyranose · ligand · 12 copies
- RM4 · beta-L-rhamnopyranose · ligand · 7 copies
- 7CV · 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose · ligand · 5 copies · chains A, B, C, D
- XYP · beta-D-xylopyranose · sugar · 24 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 15 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 12 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 11 copies
- HG · Mercury (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.82 | 0.84 | 82 | empty |
| 2 | 214 | 0.65 | 0.84 | 36 | empty |
| 3 | 206 | 0.53 | 0.77 | 33 | empty |
| 4 | 151 | 0.51 | 0.79 | 33 | empty |
| 5 | 167 | 0.51 | 0.78 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 638 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 621 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 609 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan (N-glycosylation).
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 P30328
- Elsewhere: RCSB PDB 5TIP · PDBe 5TIP · UniProt P30328
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.