Research workbench
Crystal structure of selenomethionine labelled DREP4 cide domain
Analyse Crystal structure of selenomethionine labelled DREP4 cide domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XPB
- Type
- protein
- Length
- 860 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnaation factor-related protein 4
- UniProt
- Q9V3H0
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Dnaation factor-related protein 4 | protein | 85 | 27% helix, 26% strand | Q9V3H0 |
| B | Dnaation factor-related protein 4 | protein | 88 | 26% helix, 27% strand | Q9V3H0 |
| C | Dnaation factor-related protein 4 | protein | 87 | 29% helix, 28% strand | Q9V3H0 |
| D, F, G, H, J | Dnaation factor-related protein 4 | protein | 86 | 27% helix, 28% strand | Q9V3H0 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.41 | 0.76 | 22 | empty |
| 2 | 56 | 0.39 | 0.80 | 14 | empty |
| 3 | 55 | 0.35 | 0.78 | 14 | empty |
| 4 | 60 | 0.34 | 0.77 | 15 | empty |
| 5 | 54 | 0.26 | 0.73 | 10 | empty |
Interfaces
9 interfaces between chains.
- A–B · 589 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 577 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 569 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 564 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 5XPB · Crystal Structure of Selenomethionine labelled Drep4 CIDE domain · 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
- Every structure of UniProt Q9V3H0
- Elsewhere: RCSB PDB 5XPB · PDBe 5XPB · UniProt Q9V3H0
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