MolNFT v1 · #167578 · protein
Artificial metalloproteins with dinuclear iron centers
6VP3 · Streptavidin: “Artificial metalloproteins with dinuclear iron centers”. X-ray diffraction, 1 ligand (KM3), 8 pockets (best druggability 0.62). MolNFT v1 #167578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VP3
- 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
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptavidin | protein | 122 | 8% helix, 55% 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
- ACT · Acetate ion · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.62 | 0.88 | 21 | KM3 |
| 2 | 98 | 0.62 | 0.88 | 20 | KM3 |
| 3 | 93 | 0.61 | 0.87 | 20 | KM3 |
| 4 | 93 | 0.60 | 0.87 | 20 | KM3 |
| 5 | 181 | 0.55 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1629 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1628 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 570 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 568 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 219 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6VP3 · 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 6VP3 · PDBe 6VP3 · UniProt P22629
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