MolNFT v1 · #186394 · protein + DNA
I-ONUI_E-HPD1-F final stage reengineered variant of I-onui
7RCG: “I-ONUI_E-HPD1-F final stage reengineered variant of I-onui”. X-ray diffraction, 3 ligands (NA, CA, CL), 5 pockets (best druggability 0.71). MolNFT v1 #186394 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RCG
- Type
- protein + DNA
- Length
- 339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-HPD1-F; DNA (26-mer)
- Ligands
- NA, CA, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-HPD1-F | protein | 287 | 50% helix, 22% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.71 | 0.97 | 23 | CL, NA |
| 2 | 70 | 0.62 | 0.91 | 20 | empty |
| 3 | 268 | 0.57 | 0.78 | 32 | NA |
| 4 | 129 | 0.53 | 0.82 | 27 | CL, NA |
| 5 | 76 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1503 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 1457 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 1297 Ų buried · 109 hydrogen bonds · nucleic-nucleic
Compared structures
- 7RCG · I-OnuI_e-hPD1-f final stage reengineered variant of I-OnuI · 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 7RCG · PDBe 7RCG
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