MolNFT v1 · #72532 · protein
Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP
3NBF · Heat resistant RNA dependent ATPase: “Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP”. X-ray diffraction, 2 ligands (8OD, 8OP), 5 pockets (best druggability 0.75). MolNFT v1 #72532 on GenesisL1: 3D structure…
- PDB
- 3NBF
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat resistant RNA dependent ATPase
- UniProt
- Q72GF3
- Ligands
- 8OD, 8OP
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Heat resistant RNA dependent ATPase | protein | 207 | 45% helix, 14% strand | Q72GF3 |
| B | Heat resistant RNA dependent ATPase | protein | 206 | 45% helix, 15% strand | Q72GF3 |
| D | Heat resistant RNA dependent ATPase | protein | 202 | 45% helix, 15% strand | Q72GF3 |
Ligands and binding sites
- 8OD · [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate · ligand · 6 copies · chains A, C, B, D
- 8OP · [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate · ligand · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.75 | 0.79 | 73 | empty |
| 2 | 121 | 0.42 | 0.76 | 14 | empty |
| 3 | 101 | 0.41 | 0.77 | 27 | 8OD |
| 4 | 130 | 0.38 | 0.73 | 21 | empty |
| 5 | 53 | 0.29 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 827 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 173 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 124 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 93 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3NBF · Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP · 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 Q72GF3
- Elsewhere: RCSB PDB 3NBF · PDBe 3NBF · UniProt Q72GF3
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