MolNFT v1 · #14606 · protein
Crystal structure of streptavidin double mutant S45A/D128A with biotin: cooperative hydrogen-bond interactions in the streptavidin- biotin system.
1MEP: “Crystal structure of streptavidin double mutant S45A/D128A with biotin: cooperative hydrogen-bond…”. X-ray diffraction, 1 ligand (BTN), 6 pockets (best druggability 0.68). MolNFT v1 #14606 on GenesisL1: 3D structure, binding sites…
- PDB
- 1MEP
- Type
- protein
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 119 | 5% helix, 56% strand | P22629 |
| B, C, D | Streptavidin | protein | 118 | 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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.68 | 0.82 | 49 | BTN |
| 2 | 330 | 0.67 | 0.81 | 54 | BTN |
| 3 | 119 | 0.64 | 0.87 | 25 | BTN |
| 4 | 112 | 0.63 | 0.88 | 28 | BTN |
| 5 | 146 | 0.52 | 0.80 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1662 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1637 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 535 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 216 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1MEP · Crystal Structure of Streptavidin Double Mutant S45A/D128A with Biotin: Cooperative… · 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 1MEP · PDBe 1MEP · UniProt P22629
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