MolNFT v1 · #127862 · protein
Crystal structure of streptavidin with cyclic peptide nqpwq
5N99: “Crystal structure of streptavidin with cyclic peptide nqpwq”. X-ray diffraction, 13 pockets (best druggability 0.74). MolNFT v1 #127862 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N99
- Type
- protein
- Length
- 1,511 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Asn-gln-dpr-TRP-gln
- UniProt
- P22629
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Streptavidin | protein | 122 | 7% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 123 | 7% helix, 54% strand | P22629 |
| C, E, F, H, J, L, N, P, R, T, V, X | Asn-gln-dpr-TRP-gln | protein | 5 | 0% helix, 0% strand | — |
| G | Streptavidin | protein | 121 | 7% helix, 56% strand | P22629 |
| I, K, O | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
| M, Q, Y | Streptavidin | protein | 120 | 8% helix, 57% strand | P22629 |
| S | Streptavidin | protein | 121 | 7% helix, 55% strand | P22629 |
| U | Streptavidin | protein | 122 | 10% helix, 55% strand | P22629 |
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.74 | 0.77 | 87 | empty |
| 2 | 473 | 0.70 | 0.81 | 53 | empty |
| 3 | 467 | 0.69 | 0.80 | 54 | empty |
| 4 | 536 | 0.68 | 0.79 | 62 | empty |
| 5 | 514 | 0.68 | 0.79 | 61 | empty |
Interfaces
57 interfaces between chains.
- K–Q · 1647 Ų buried · 30 hydrogen bonds · protein-protein
- G–I · 1632 Ų buried · 33 hydrogen bonds · protein-protein
- O–Y · 1625 Ų buried · 27 hydrogen bonds · protein-protein
- A–M · 1624 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1603 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 d-amino (D-amino acid).
Compared structures
- 5N99 · CRYSTAL STRUCTURE OF STREPTAVIDIN with cyclic peptide NQpWQ · 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 5N99 · PDBe 5N99 · UniProt P22629
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