Research workbench
Engbf darpin fusion 4B B6
Analyse Engbf darpin fusion 4B B6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QEV
- Type
- protein
- Length
- 1,361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pega domain-containing PROTEIN,PEGA domain-containing PROTEIN,ENGBF darpin fusion B6…
- UniProt
- A0A414FD23
- Ligands
- MN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pega domain-containing PROTEIN,PEGA domain-containing PROTEIN,ENGBF darpin fusion B6 complex | protein | 1346 | 22% helix, 31% strand | A0A414FD23 |
| D | Pro-lys-ser-ile-arg-ile-gly-pro-gly-gln-ala-phe-tyr-ala- dpr | protein | 15 | 0% helix, 0% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.81 | 0.96 | 47 | empty |
| 2 | 72 | 0.75 | 0.99 | 25 | empty |
| 3 | 692 | 0.73 | 0.80 | 73 | empty |
| 4 | 191 | 0.51 | 0.77 | 34 | empty |
| 5 | 231 | 0.50 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- B–D · 737 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 d-amino (D-amino acid).
Compared structures
- 6QEV · EngBF DARPin Fusion 4b B6 · the same entry in another collection · chain B against B, 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 A0A414FD23
- Elsewhere: RCSB PDB 6QEV · PDBe 6QEV · UniProt A0A414FD23
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