MolNFT v1 · #74676 · protein
Crystal structure of a pts dependent N-acetyl-galactosamine-iib component (agav, SPY_0631) from streptococcus pyogenes at 1.65 a resolution
3P3V · Pts system, N-acetylgalactosamine-specific iib component: “Crystal structure of a pts dependent N-acetyl-galactosamine-iib component (agav, SPY_0631) from streptococcus…”. X-ray diffraction, 4 pockets (best druggability 0.71).…
- PDB
- 3P3V
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pts system, N-acetylgalactosamine-specific iib component
- EC
- 2.7.1.69
- UniProt
- Q9A0T4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pts system, N-acetylgalactosamine-specific iib component (EC 2.7.1.69) | protein | 162 | 40% helix, 24% strand | Q9A0T4 |
| B | Pts system, N-acetylgalactosamine-specific iib component (EC 2.7.1.69) | protein | 163 | 38% helix, 23% strand | Q9A0T4 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.71 | 0.80 | 55 | PEG |
| 2 | 69 | 0.56 | 0.88 | 24 | empty |
| 3 | 129 | 0.46 | 0.78 | 21 | empty |
| 4 | 52 | 0.34 | 0.78 | 13 | PGE |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3P3V · Crystal structure of a PTS dependent N-acetyl-galactosamine-IIB component (agaV… · 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 Q9A0T4
- Elsewhere: RCSB PDB 3P3V · PDBe 3P3V · UniProt Q9A0T4
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