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Crystal structure of streptavidin with peptide D-amino acid containing peptide gyglanvdessg
Analyse Crystal structure of streptavidin with peptide D-amino acid containing peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N8J
- Type
- protein
- Length
- 506 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Gly-dty-gly-dle-dal-dsg-dva-das-dgl-dsn-dsn-gly
- UniProt
- P22629
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 122 | 7% helix, 54% strand | P22629 |
| B, C, D | Streptavidin | protein | 120 | 8% helix, 56% strand | P22629 |
| P | Gly-dty-gly-dle-dal-dsg-dva-das-dgl-dsn-dsn-gly | protein | 9 | 56% helix, 0% strand | — |
| O | Gly-dty-gly-dle-dal-dsg-dva-das-dgl-dsn-dsn-gly | protein | 7 | 57% helix, 0% strand | — |
| E | Gly-dty-gly-dle-dal-dsg-dva-das-dgl-dsn-dsn-gly | protein | 8 | 50% helix, 0% strand | — |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.73 | 0.80 | 81 | IPA |
| 2 | 492 | 0.69 | 0.80 | 47 | empty |
| 3 | 76 | 0.32 | 0.74 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1644 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1616 Ų buried · 29 hydrogen bonds · protein-protein
- D–P · 551 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 532 Ų buried · 7 hydrogen bonds · protein-protein
- A–O · 511 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 d-amino (D-amino acid).
Compared structures
- 5N8J · CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid containing peptide… · 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 5N8J · PDBe 5N8J · UniProt P22629
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