MolNFT v1 · #114205 · protein
Crystal structure of ALIS4-streptavidin complex
5B5G: “Crystal structure of ALIS4-streptavidin complex”. X-ray diffraction, 2 ligands (6FX, SO3), 5 pockets (best druggability 0.67). MolNFT v1 #114205 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B5G
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- 6FX, SO3
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptavidin | protein | 120 | 3% helix, 57% strand | P22629 |
Ligands and binding sites
- 6FX · methyl 5-(4-oxidanylidene-5~{H}-furo[3,2-c]pyridin-2-yl)pyridine-3-carboxylate · ligand · 2 copies · chains A, C, D
- SO3 · Sulfite ion · ion · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.67 | 0.82 | 49 | SO3 |
| 2 | 383 | 0.64 | 0.79 | 48 | SO3 |
| 3 | 340 | 0.63 | 0.79 | 38 | SO3 |
| 4 | 202 | 0.51 | 0.76 | 20 | 6FX |
| 5 | 150 | 0.47 | 0.76 | 19 | 6FX |
Interfaces
6 interfaces between chains.
- A–D · 1628 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1620 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 389 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 213 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5B5G · Crystal structure of ALiS4-Streptavidin 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 5B5G · PDBe 5B5G · UniProt P22629
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