Research workbench
The structure of the streptococcus gordonii surface protein sspb in complex with tev peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin
Analyse The structure of the streptococcus gordonii surface protein sspb in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UBV
- Type
- protein
- Length
- 1,573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface protein adhesin
- UniProt
- C9E3B4
- Ligands
- SNZ, CA, NA, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Surface protein adhesin | protein | 392 | 21% helix, 33% strand | C9E3B4 |
| B | Surface protein adhesin | protein | 394 | 22% helix, 32% strand | C9E3B4 |
| C | Surface protein adhesin | protein | 399 | 21% helix, 31% strand | C9E3B4 |
| D | Surface protein adhesin | protein | 388 | 19% helix, 32% strand | C9E3B4 |
Ligands and binding sites
- SNZ · N-(3,4-dihydroxyphenyl)-N'-[2-(3,4-dihydroxyphenyl) ethyl]urea · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.78 | 0.80 | 141 | SO4, SNZ, NA, EDO |
| 2 | 1013 | 0.77 | 0.80 | 121 | CA, SNZ, NA, SO4 |
| 3 | 497 | 0.65 | 0.77 | 48 | CA, SNZ, NA, EDO |
| 4 | 425 | 0.64 | 0.78 | 45 | CA, SNZ, EDO |
| 5 | 147 | 0.54 | 0.81 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 702 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 620 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6UBV · The structure of the Streptococcus gordonii surface protein SspB in complex with TEV… · 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 C9E3B4
- Elsewhere: RCSB PDB 6UBV · PDBe 6UBV · UniProt C9E3B4
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