Research workbench
Trans-divalent streptavidin with love-hate ligand 4
Analyse Trans-divalent streptavidin with love-hate ligand 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CPH
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- LH4
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 118 | 5% helix, 58% strand | P22629 |
| B, C | Streptavidin | protein | 120 | 8% helix, 55% strand | P22629 |
| D | Streptavidin | protein | 118 | 8% helix, 58% strand | P22629 |
Ligands and binding sites
- LH4 · 5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4- d]imidazolidin-4-yl]-N'-{2,6-bis[4-(morpholine-4- sulfonyl)phenyl]phenyl}pentanehydrazide · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.55 | 0.80 | 33 | empty |
| 2 | 148 | 0.54 | 0.81 | 24 | empty |
| 3 | 174 | 0.52 | 0.79 | 24 | empty |
| 4 | 164 | 0.52 | 0.79 | 27 | empty |
| 5 | 159 | 0.50 | 0.77 | 19 | LH4 |
Interfaces
6 interfaces between chains.
- B–D · 1618 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1612 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 430 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 215 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4CPH · trans-divalent streptavidin with love-hate ligand 4 · 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 4CPH · PDBe 4CPH · UniProt P22629
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