MolNFT v1 · #139761 · protein
Crystal structure of DREP4 cide domain
5XPC · Dnaation factor-related protein 4: “Crystal structure of DREP4 cide domain”. X-ray diffraction, 3 pockets (best druggability 0.37). MolNFT v1 #139761 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XPC
- Type
- protein
- Length
- 433 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnaation factor-related protein 4
- UniProt
- Q9V3H0
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dnaation factor-related protein 4 | protein | 85 | 27% helix, 27% strand | Q9V3H0 |
| B | Dnaation factor-related protein 4 | protein | 88 | 30% helix, 26% strand | Q9V3H0 |
| C | Dnaation factor-related protein 4 | protein | 86 | 28% helix, 27% strand | Q9V3H0 |
| D | Dnaation factor-related protein 4 | protein | 87 | 29% helix, 26% strand | Q9V3H0 |
| E | Dnaation factor-related protein 4 | protein | 87 | 28% helix, 25% strand | Q9V3H0 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.37 | 0.78 | 18 | GOL |
| 2 | 66 | 0.36 | 0.77 | 15 | empty |
| 3 | 95 | 0.33 | 0.72 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 623 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 551 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 551 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 539 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5XPC · Crystal Structure of 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 5XPC · PDBe 5XPC · UniProt Q9V3H0
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