MolNFT v1 · #118041 · protein
Crystal structure of the srpa adhesin R347E mutant from streptococcus sanguinis
5EQ4 · Platelet-binding glycoprotein: “Crystal structure of the srpa adhesin R347E mutant from streptococcus sanguinis”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.75). MolNFT v1 #118041 on GenesisL1: 3D structure…
- PDB
- 5EQ4
- Type
- protein
- Length
- 770 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-binding glycoprotein
- UniProt
- A3CM52
- Ligands
- CA
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-binding glycoprotein | protein | 188 | 12% helix, 35% strand | A3CM52 |
| B | Platelet-binding glycoprotein | protein | 195 | 12% helix, 36% strand | A3CM52 |
| C | Platelet-binding glycoprotein | protein | 193 | 10% helix, 36% strand | A3CM52 |
| D | Platelet-binding glycoprotein | protein | 194 | 11% helix, 38% strand | A3CM52 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.75 | 0.80 | 83 | ACT |
| 2 | 109 | 0.37 | 0.74 | 18 | empty |
| 3 | 76 | 0.31 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 577 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 282 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 154 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EQ4 · Crystal structure of the SrpA adhesin R347E mutant from Streptococcus sanguinis · 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 A3CM52
- Elsewhere: RCSB PDB 5EQ4 · PDBe 5EQ4 · UniProt A3CM52
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