MolNFT v1 · #103360 · protein
DBR1 in complex with guanosine-5'-monophosphate
4PEG · RNA lariat debranching enzyme, putative: “DBR1 in complex with guanosine-5'-monophosphate”. X-ray diffraction, 3 ligands (5GP, MN, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #103360 on GenesisL1: 3D structure, binding…
- PDB
- 4PEG
- Type
- protein
- Length
- 1,746 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative
- UniProt
- C4M1P9
- Ligands
- 5GP, MN, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | RNA lariat debranching enzyme, putative | protein | 349 | 36% helix, 22% strand | C4M1P9 |
| C | RNA lariat debranching enzyme, putative | protein | 350 | 37% helix, 21% strand | C4M1P9 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, E
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.78 | 0.80 | 81 | GOL |
| 2 | 787 | 0.77 | 0.81 | 74 | empty |
| 3 | 54 | 0.73 | 0.99 | 17 | empty |
| 4 | 52 | 0.73 | 1.00 | 18 | empty |
| 5 | 52 | 0.72 | 0.99 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 777 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 668 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 645 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 349 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 276 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4PEG · Dbr1 in complex with guanosine-5'-monophosphate · 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 4PEG · PDBe 4PEG · UniProt C4M1P9
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