Research workbench
The N-terminal domain of the streptococcus pyogenes pilus tip adhesin cpa
Analyse The N-terminal domain of the streptococcus pyogenes pilus tip adhesin cpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C0Z
- Type
- protein
- Length
- 2,488 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancillary protein 2
- UniProt
- S5FV19
- Ligands
- SPD, CL, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, H | Ancillary protein 2 | protein | 208 | 30% helix, 19% strand | S5FV19 |
| B | Ancillary protein 2 | protein | 208 | 32% helix, 19% strand | S5FV19 |
| C | Ancillary protein 2 | protein | 205 | 31% helix, 19% strand | S5FV19 |
| E | Ancillary protein 2 | protein | 206 | 31% helix, 19% strand | S5FV19 |
| F, L | Ancillary protein 2 | protein | 209 | 30% helix, 19% strand | S5FV19 |
| G, I, J | Ancillary protein 2 | protein | 207 | 30% helix, 19% strand | S5FV19 |
| K | Ancillary protein 2 | protein | 206 | 31% helix, 18% strand | S5FV19 |
Ligands and binding sites
- SPD · Spermidine · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 14 copies · chains A, B, H, C, D, E, F, G, I, J, K, L
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, J, F
- GOL · Glycerol · additive · 3 copies · chains C, D, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.82 | 0.83 | 117 | empty |
| 2 | 345 | 0.79 | 0.89 | 39 | empty |
| 3 | 283 | 0.76 | 0.88 | 48 | empty |
| 4 | 313 | 0.76 | 0.87 | 52 | empty |
| 5 | 490 | 0.75 | 0.83 | 53 | empty |
Interfaces
18 interfaces between chains.
- E–F · 1262 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 1232 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1218 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1214 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 4C0Z · The N-terminal domain of the Streptococcus pyogenes pilus tip adhesin Cpa · the same entry in another collection · chain L against L, 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 S5FV19
- Elsewhere: RCSB PDB 4C0Z · PDBe 4C0Z · UniProt S5FV19
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