MolNFT v1 · #103359 · protein
DBR1 in complex with sulfate
4PEF · RNA lariat debranching enzyme, putative: “DBR1 in complex with sulfate”. X-ray diffraction, 2 ligands (MN, SO4), 20 pockets (best druggability 0.77). MolNFT v1 #103359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PEF
- Type
- protein
- Length
- 1,745 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative
- UniProt
- C4M1P9
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA lariat debranching enzyme, putative | protein | 349 | 38% helix, 21% strand | C4M1P9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.77 | 0.80 | 79 | empty |
| 2 | 686 | 0.75 | 0.80 | 51 | GOL |
| 3 | 55 | 0.73 | 0.99 | 18 | empty |
| 4 | 50 | 0.72 | 0.99 | 16 | empty |
| 5 | 50 | 0.71 | 0.99 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–C · 796 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 658 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 641 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 381 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 236 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4PEF · Dbr1 in complex with sulfate · 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 C4M1P9
- Elsewhere: RCSB PDB 4PEF · PDBe 4PEF · UniProt C4M1P9
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