Research workbench
Crystal structure of the C-terminal domain of Streptococcus mutans surface protein SpaP
Analyse Crystal structure of the C-terminal domain of Streptococcus mutans surface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OPU
- Type
- protein
- Length
- 2,029 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.181
- Source
- Streptococcus mutans
- Molecule
- SpaP
- Ligands
- CA
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.181 · 3 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | SpaP | protein | 338 | 13% helix, 44% strand | — |
| C | SpaP | protein | 337 | 12% helix, 44% strand | — |
| D, E | SpaP | protein | 339 | 13% helix, 44% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.82 | 0.83 | 114 | empty |
| 2 | 952 | 0.78 | 0.81 | 106 | empty |
| 3 | 155 | 0.74 | 0.92 | 27 | empty |
| 4 | 1025 | 0.73 | 0.76 | 104 | empty |
| 5 | 1028 | 0.72 | 0.76 | 102 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1267 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1200 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 566 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 448 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 isopeptide (isopeptide).
Compared structures
- 3OPU · Crystal structure of the C-terminal domain of streptococcus mutans surface protein spap · 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
- Elsewhere: RCSB PDB 3OPU · PDBe 3OPU
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