MolNFT v1 · #156597 · protein
Wild-type streptavidin in complex with biotin solved by native sad with data collected at 6 kev
6M9B: “Wild-type streptavidin in complex with biotin solved by native sad with data collected at 6 kev”. X-ray diffraction, 1 ligand (BTN), 5 pockets (best druggability 0.69). MolNFT v1 #156597 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6M9B
- Type
- protein
- Length
- 477 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 119 | 5% helix, 55% strand | P22629 |
| B, D | Streptavidin | protein | 119 | 5% helix, 55% strand | P22629 |
| C | Streptavidin | protein | 120 | 3% helix, 56% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, D, B, C
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 | 257 | 0.69 | 0.84 | 50 | BTN |
| 2 | 269 | 0.68 | 0.83 | 49 | BTN |
| 3 | 315 | 0.64 | 0.81 | 47 | empty |
| 4 | 147 | 0.54 | 0.81 | 24 | empty |
| 5 | 180 | 0.52 | 0.79 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1666 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1594 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 542 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6M9B · Wild-type streptavidin in complex with biotin solved by native SAD with data collected at… · 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 6M9B · PDBe 6M9B · UniProt P22629
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