MolNFT v1 · #123208 · protein
Sfx structure of corestreptavidin-selenobiotin complex
5JD2: “Sfx structure of corestreptavidin-selenobiotin complex”. X-ray diffraction, 1 ligand (BYY), 6 pockets (best druggability 0.70). MolNFT v1 #123208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JD2
- Type
- protein
- Length
- 474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BYY
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Streptavidin | protein | 119 | 3% helix, 56% strand | P22629 |
| C | Streptavidin | protein | 120 | 3% helix, 55% strand | P22629 |
| D | Streptavidin | protein | 116 | 5% helix, 59% strand | P22629 |
Ligands and binding sites
- BYY · 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.70 | 0.81 | 68 | BYY |
| 2 | 93 | 0.63 | 0.89 | 21 | BYY |
| 3 | 106 | 0.61 | 0.87 | 25 | BYY |
| 4 | 130 | 0.60 | 0.85 | 27 | BYY |
| 5 | 164 | 0.53 | 0.80 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1635 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1627 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 515 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 206 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5JD2 · SFX structure of corestreptavidin-selenobiotin complex · 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 P22629
- Elsewhere: RCSB PDB 5JD2 · PDBe 5JD2 · UniProt P22629
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