MolNFT v1 · #127827 · protein
Crystal structure of streptavidin with peptide gnsfddwlaskg
5N89: “Crystal structure of streptavidin with peptide gnsfddwlaskg”. X-ray diffraction, 1 ligand (NH2), 10 pockets (best druggability 0.77). MolNFT v1 #127827 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N89
- Type
- protein
- Length
- 1,065 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Gly-asn-ser-phe-asp-asp-TRP-leu-ala-ser-lys-gly-NH2
- UniProt
- P22629
- Ligands
- NH2
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 121 | 5% helix, 55% strand | P22629 |
| B, D, F, H, M | Streptavidin | protein | 122 | 7% helix, 55% strand | P22629 |
| C, E, G, I, J, N, P | Gly-asn-ser-phe-asp-asp-TRP-leu-ala-ser-lys-gly-NH2 | protein | 12 | 75% helix, 0% strand | — |
| K | Streptavidin | protein | 119 | 8% helix, 56% strand | P22629 |
| L | Gly-asn-ser-phe-asp-asp-TRP-leu-ala-ser-lys-gly-NH2 | protein | 11 | 82% helix, 0% strand | — |
| O | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
Ligands and binding sites
- NH2 · Amino group · ion · 8 copies · chains B, C, D, E, N, F, G, A, I, H, J, K, L, M, O, P
- GOL · Glycerol · additive · 8 copies · chains A, I, B, C, D, E, F, G, H, J, K, L, O, M, N, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.77 | 0.80 | 110 | NH2, GOL |
| 2 | 530 | 0.73 | 0.81 | 61 | GOL |
| 3 | 504 | 0.68 | 0.79 | 63 | empty |
| 4 | 215 | 0.57 | 0.80 | 28 | empty |
| 5 | 254 | 0.56 | 0.78 | 35 | empty |
Interfaces
33 interfaces between chains.
- H–K · 1624 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1619 Ų buried · 27 hydrogen bonds · protein-protein
- M–O · 1616 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1610 Ų buried · 27 hydrogen bonds · protein-protein
- O–P · 467 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5N89 · Crystal structure of streptavidin with peptide gnsfddwlaskg · 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 5N89 · PDBe 5N89 · UniProt P22629
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