MolNFT v1 · #186391 · protein + DNA
Second stage reengineered variant of I-onui targeting human PD1 gene with activity enhancing substitutions
7RCD · I-ONUI_E-HPD1-C: “Second stage reengineered variant of I-onui targeting human PD1 gene with activity enhancing substitutions”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.72). MolNFT v1 #186391 on GenesisL1: 3D…
- PDB
- 7RCD
- 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-C; DNA (26-mer)
- Ligands
- CA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-HPD1-C | protein | 287 | 49% helix, 21% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C
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 | 99 | 0.72 | 0.94 | 29 | empty |
| 2 | 164 | 0.57 | 0.82 | 33 | empty |
| 3 | 166 | 0.53 | 0.80 | 27 | empty |
| 4 | 222 | 0.51 | 0.77 | 23 | empty |
| 5 | 111 | 0.41 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1402 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 1341 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 1290 Ų buried · 123 hydrogen bonds · nucleic-nucleic
Compared structures
- 7RCD · Second stage reengineered variant of I-OnuI targeting human PD1 gene with activity… · 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 7RCD · PDBe 7RCD
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