MolNFT v1 · #117354 · protein + DNA
I-smami bound to uncleaved DNA target in the presence of calcium ions
5E5O · I-smami laglidadg endonuclease: “I-smami bound to uncleaved DNA target in the presence of calcium ions”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.62). MolNFT v1 #117354 on GenesisL1: 3D structure, binding…
- PDB
- 5E5O
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-smami laglidadg endonuclease; DNA (25-mer); Top strand DNA (25-mer)
- UniProt
- F7WD42
- Ligands
- CA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-smami laglidadg endonuclease | protein | 294 | 49% helix, 20% strand | F7WD42 |
| B | DNA (25-mer) | dna | 25 | — | — |
| C | Top strand DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 7 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.62 | 0.85 | 28 | CA, EDO |
| 2 | 76 | 0.53 | 0.86 | 20 | CA |
| 3 | 131 | 0.40 | 0.75 | 16 | empty |
| 4 | 83 | 0.35 | 0.76 | 17 | empty |
| 5 | 50 | 0.27 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1534 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 1481 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 1228 Ų buried · 96 hydrogen bonds · nucleic-nucleic
Compared structures
- 5E5O · I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions · 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 F7WD42
- Elsewhere: RCSB PDB 5E5O · PDBe 5E5O · UniProt F7WD42
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