Research workbench
Crystal structure of a vflip-ikkgamma stapled peptide dimer
Analyse Crystal structure of a vflip-ikkgamma stapled peptide dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LDE
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein G,VIRAL flice protein; Inhibitor of kappa light…
- UniProt
- P19909, F5HEZ4, D3DWY2
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin G-binding protein G,VIRAL flice protein | protein | 221 | 59% helix, 6% strand | P19909, F5HEZ4 |
| B | Immunoglobulin G-binding protein G,VIRAL flice protein | protein | 225 | 60% helix, 5% strand | P19909, F5HEZ4 |
| R, S | Inhibitor of kappa light polypeptide gene enhancer in B- cells, kinase gamma, isoform CRA_A | protein | 20 | 80% helix, 0% strand | D3DWY2 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.42 | 0.78 | 16 | empty |
| 2 | 88 | 0.39 | 0.77 | 25 | empty |
| 3 | 72 | 0.35 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–R · 503 Ų buried · 2 hydrogen bonds · protein-protein
- A–S · 500 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 156 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5LDE · Crystal structure of a vFLIP-IKKgamma stapled peptide dimer · the same entry in another collection · chain A against A, TM-score 1.00
- P19909 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P19909) · a predicted model of the same protein · chain A against A, TM-score 0.25
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 P19909
- Every structure of UniProt F5HEZ4
- Every structure of UniProt D3DWY2
- Elsewhere: RCSB PDB 5LDE · PDBe 5LDE · UniProt P19909 · UniProt F5HEZ4 · UniProt D3DWY2
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