MolNFT v1 · #186392 · protein + DNA
Third stage reengineered variant of I-onui with specificity enhancing substitutions
7RCE · I-ONUI_E-HPD1-D: “Third stage reengineered variant of I-onui with specificity enhancing substitutions”. X-ray diffraction, 2 ligands (CA, NA), 6 pockets (best druggability 0.68). MolNFT v1 #186392 on GenesisL1: 3D structure, binding…
- PDB
- 7RCE
- Type
- protein + DNA
- Length
- 337 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-HPD1-D; DNA (26-mer)
- Ligands
- CA, NA
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-HPD1-D | protein | 285 | 49% helix, 20% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.68 | 0.98 | 19 | empty |
| 2 | 74 | 0.64 | 0.92 | 18 | empty |
| 3 | 82 | 0.51 | 0.84 | 21 | empty |
| 4 | 170 | 0.50 | 0.79 | 22 | empty |
| 5 | 110 | 0.48 | 0.81 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1356 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1335 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 1296 Ų buried · 122 hydrogen bonds · nucleic-nucleic
Compared structures
- 7RCE · Third stage reengineered variant of I-OnuI with specificity enhancing substitutions · 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
- Elsewhere: RCSB PDB 7RCE · PDBe 7RCE
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