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Crystal structure of the N-terminal domain of the streptococcus gordonii adhesin SGO0707
Analyse Crystal structure of the N-terminal domain of the streptococcus gordonii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IGB
- Type
- protein
- Length
- 1,710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lpxtg cell wall surface protein
- UniProt
- A8AW49
- Ligands
- NA, SO4
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lpxtg cell wall surface protein | protein | 426 | 6% helix, 50% strand | A8AW49 |
| B | Lpxtg cell wall surface protein | protein | 435 | 7% helix, 51% strand | A8AW49 |
| C | Lpxtg cell wall surface protein | protein | 433 | 7% helix, 51% strand | A8AW49 |
| D | Lpxtg cell wall surface protein | protein | 416 | 8% helix, 50% strand | A8AW49 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.73 | 0.77 | 86 | empty |
| 2 | 473 | 0.65 | 0.78 | 43 | ACT |
| 3 | 146 | 0.63 | 0.86 | 25 | empty |
| 4 | 562 | 0.61 | 0.74 | 51 | empty |
| 5 | 415 | 0.59 | 0.75 | 50 | empty |
Interfaces
4 interfaces between chains.
- A–C · 970 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 947 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 713 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 258 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4IGB · Crystal structure of the N-terminal domain of the Streptococcus gordonii adhesin Sgo0707 · 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 A8AW49
- Elsewhere: RCSB PDB 4IGB · PDBe 4IGB · UniProt A8AW49
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