MolNFT v1 · #150015 · protein
Wildtype core-streptavidin with a conjugated biotinylated pyrrolidine
6GH7: “Wildtype core-streptavidin with a conjugated biotinylated pyrrolidine”. X-ray diffraction, 1 ligand (EYW), 5 pockets (best druggability 0.68). MolNFT v1 #150015 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GH7
- Type
- protein
- Length
- 477 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- EYW
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
| B | Streptavidin | protein | 119 | 3% helix, 56% strand | P22629 |
| C | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
| D | Streptavidin | protein | 118 | 3% helix, 57% strand | P22629 |
Ligands and binding sites
- EYW · 5-[(3~{A}~{S},4~{S},6~{A}~{R})-2-oxidanylidene-1,3, 3~{A},4,6,6~{A}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[(3~{R})-pyrrolidin-3-yl]pentanamide · ligand · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.68 | 0.83 | 49 | EYW |
| 2 | 413 | 0.64 | 0.78 | 62 | empty |
| 3 | 356 | 0.64 | 0.79 | 55 | empty |
| 4 | 101 | 0.60 | 0.86 | 25 | EYW |
| 5 | 136 | 0.56 | 0.82 | 25 | EYW |
Interfaces
6 interfaces between chains.
- C–D · 1645 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1611 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 545 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GH7 · WILDTYPE CORE-STREPTAVIDIN WITH a conjugated BIOTINYLATED PYRROLIDINE · 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 6GH7 · PDBe 6GH7 · UniProt P22629
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