MolNFT v1 · #186390 · protein + DNA
First stage engineered variant of I-onui after initial reassembly
7RCC · I-ONUI_E-HPD1-B: “First stage engineered variant of I-onui after initial reassembly”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.79). MolNFT v1 #186390 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7RCC
- Type
- protein + DNA
- Length
- 997 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-HPD1-B; DNA (26-mer)
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-HPD1-B | protein | 281 | 49% helix, 21% strand | — |
| B, E, H | DNA (26-mer) | dna | 26 | — | — |
| C, F, I | DNA (26-mer) | dna | 26 | — | — |
| D | I-ONUI_E-HPD1-B | protein | 279 | 49% helix, 19% strand | — |
| G | I-ONUI_E-HPD1-B | protein | 281 | 49% helix, 19% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, E, F, B, C, D, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.79 | 0.83 | 71 | empty |
| 2 | 689 | 0.74 | 0.80 | 65 | empty |
| 3 | 222 | 0.70 | 0.87 | 42 | empty |
| 4 | 200 | 0.70 | 0.87 | 36 | empty |
| 5 | 68 | 0.64 | 0.93 | 21 | CA |
Interfaces
17 interfaces between chains.
- C–D · 1408 Ų buried · 38 hydrogen bonds · protein-nucleic
- G–I · 1401 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–F · 1386 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–E · 1369 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–D · 1327 Ų buried · 31 hydrogen bonds · protein-nucleic
Compared structures
- 7RCC · First stage engineered variant of I-OnuI after initial reassembly · 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 7RCC · PDBe 7RCC
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