MolNFT v1 · #179647 · protein
Artificial metalloproteins with dinuclear iron centers
7KBZ · Streptavidin: “Artificial metalloproteins with dinuclear iron centers”. X-ray diffraction, 2 ligands (KM3, CYN), 7 pockets (best druggability 0.64). MolNFT v1 #179647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KBZ
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- KM3, CYN
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptavidin | protein | 122 | 6% helix, 54% strand | P22629 |
Ligands and binding sites
- KM3 · {N-(4-{bis[(pyridin-2-yl-kappaN)methyl]amino-kappaN}butyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}iron(3+) · ligand · 4 copies · chains A, D, B, C
- CYN · Cyanide ion · ion · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.64 | 0.79 | 66 | empty |
| 2 | 98 | 0.63 | 0.88 | 21 | KM3 |
| 3 | 103 | 0.61 | 0.87 | 21 | KM3 |
| 4 | 90 | 0.61 | 0.88 | 21 | KM3 |
| 5 | 93 | 0.60 | 0.87 | 20 | KM3 |
Interfaces
6 interfaces between chains.
- B–D · 1618 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1610 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 580 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 573 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7KBZ · Artificial Metalloproteins with Dinuclear Iron Centers · 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 7KBZ · PDBe 7KBZ · UniProt P22629
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.