Research workbench
Modulating protein-protein interactions with visible light peptide backbone switches
Analyse Modulating protein-protein interactions with visible light peptide backbone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IAM
- Type
- protein
- Length
- 320 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Ser-ala-arg-ala-XY5-val-his-leu-arg-lys-ser-ala; Small…
- UniProt
- P61964, G2XKQ0
- Ligands
- XY5, K, NA
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 306 | 0% helix, 52% strand | P61964 |
| B | Ser-ala-arg-ala-XY5-val-his-leu-arg-lys-ser-ala | protein | 10 | 0% helix, 0% strand | — |
| C | Small ubiquitin-related modifier 5 | protein | 4 | 0% helix, 0% strand | G2XKQ0 |
Ligands and binding sites
- XY5 · 2-[[(5~{Z})-8-azanyl-11,12-dihydrobenzo[c][1, 2]benzodiazocin-3-yl]amino]ethanal · ligand · chains A, B
- K · Potassium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.75 | 0.84 | 44 | empty |
| 2 | 52 | 0.57 | 0.90 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 614 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6IAM · Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches · the same entry in another collection · chain A against A, TM-score 1.00
- G2XKQ0 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 5 (G2XKQ0) · a predicted model of the same protein · chain C against A, TM-score 0.83
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 P61964
- Every structure of UniProt G2XKQ0
- Elsewhere: RCSB PDB 6IAM · PDBe 6IAM · UniProt P61964 · UniProt G2XKQ0
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