Research workbench
Crystal structure of streptavidin mutant (M2) where the L3, 4 loop was replace by that of avidin
Analyse Crystal structure of streptavidin mutant (M2) where the L3, 4 loop was replace… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RXJ
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BNI
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 115 | 5% helix, 58% strand | P22629 |
| B | Streptavidin | protein | 115 | 5% helix, 59% strand | P22629 |
| C | Streptavidin | protein | 112 | 5% helix, 61% strand | P22629 |
| D | Streptavidin | protein | 114 | 5% helix, 58% strand | P22629 |
Ligands and binding sites
- BNI · 5-(2-oxo-hexahydro-thieno[3,4-d]imidazol-6-yl)-pentanoic acid (4-nitro-phenyl)-amide · ligand · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.65 | 0.79 | 51 | empty |
| 2 | 169 | 0.53 | 0.80 | 29 | empty |
| 3 | 178 | 0.53 | 0.79 | 25 | empty |
| 4 | 136 | 0.48 | 0.78 | 19 | BNI |
| 5 | 122 | 0.47 | 0.78 | 18 | BNI |
Interfaces
6 interfaces between chains.
- A–B · 1646 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1618 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 432 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 215 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1RXJ · Crystal structure of streptavidin mutant (M2) where the L3,4 loop was replace by that of… · 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 1RXJ · PDBe 1RXJ · UniProt P22629
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