MolNFT v1 · #112503 · protein
Using molecular dynamics simulations to predict domain swapping of computationally designed protein variants
4ZN8 · Computationally modified engrailed homeodomain: “Using molecular dynamics simulations to predict domain swapping of computationally designed protein variants”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.82).…
- PDB
- 4ZN8
- Type
- protein
- Length
- 192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Computationally modified engrailed homeodomain
- Ligands
- K
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Computationally modified engrailed homeodomain | protein | 51 | 71% helix, 0% strand | — |
| B | Computationally modified engrailed homeodomain | protein | 49 | 73% helix, 0% strand | — |
| C | Computationally modified engrailed homeodomain | protein | 46 | 76% helix, 0% strand | — |
| D | Computationally modified engrailed homeodomain | protein | 46 | 80% helix, 0% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.82 | 0.95 | 24 | empty |
| 2 | 231 | 0.55 | 0.78 | 25 | empty |
| 3 | 258 | 0.51 | 0.75 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1251 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1122 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 612 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 603 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4ZN8 · Using molecular dynamics simulations to predict domain swapping of computationally… · 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 4ZN8 · PDBe 4ZN8
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