Research workbench
De novo design of novel covalent constrained meso-size peptide scaffolds with unique tertiary structures
Analyse De novo design of novel covalent constrained meso-size peptide scaffolds with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V2O
- Type
- protein
- Length
- 360 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TP2
- Ligands
- TMM, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | TP2 | protein | 60 | 75% helix, 0% strand | — |
Ligands and binding sites
- TMM · 1,3,5-benzenetricarboxylic acid · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, C, D, F
- 2PE · Nonaethylene glycol · additive · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 copies · chains C, D, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.65 | 0.76 | 68 | SO4 |
| 2 | 96 | 0.61 | 0.88 | 19 | GOL |
| 3 | 86 | 0.47 | 0.81 | 17 | empty |
| 4 | 70 | 0.41 | 0.80 | 17 | empty |
| 5 | 76 | 0.36 | 0.76 | 16 | SO4 |
Interfaces
9 interfaces between chains.
- A–C · 856 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 736 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 729 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 444 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 386 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 covalent (covalent ligand).
Compared structures
- 5V2O · De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique… · 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
- Elsewhere: RCSB PDB 5V2O · PDBe 5V2O
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