MolNFT v1 · #62495 · protein + DNA
Crystal structure of Y2 I-anii variant (F13Y/S111Y)/DNA complex with calcium
3EH8 · Intron-encoded DNA endonuclease I-anii: “Crystal structure of Y2 I-anii variant (F13Y/S111Y)/DNA complex with calcium”. X-ray diffraction, 1 ligand (CA), 15 pockets (best druggability 0.67). MolNFT v1 #62495 on GenesisL1: 3D…
- PDB
- 3EH8
- Type
- protein + DNA
- Length
- 948 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intron-encoded DNA endonuclease I-anii; 31-mer
- EC
- 3.1.-.-
- UniProt
- P03880
- Ligands
- CA
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Intron-encoded DNA endonuclease I-anii (EC 3.1.-.-) | protein | 254 | 44% helix, 23% strand | P03880 |
| B, E, H | 31-mer | dna | 31 | — | — |
| C, F, I | 31-mer | dna | 31 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.67 | 0.78 | 35 | empty |
| 2 | 257 | 0.57 | 0.79 | 34 | empty |
| 3 | 251 | 0.57 | 0.79 | 32 | empty |
| 4 | 287 | 0.56 | 0.77 | 38 | empty |
| 5 | 260 | 0.54 | 0.76 | 33 | empty |
Interfaces
16 interfaces between chains.
- H–I · 1544 Ų buried · 130 hydrogen bonds · nucleic-nucleic
- B–C · 1493 Ų buried · 132 hydrogen bonds · nucleic-nucleic
- E–F · 1490 Ų buried · 125 hydrogen bonds · nucleic-nucleic
- D–F · 1430 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–E · 1427 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 3EH8 · Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium · the same entry in another collection · chain I against I, TM-score 1.00
- P03880 · AlphaFold monomer V2.0 prediction for intron-encoded DNA endonuclease I-anii (P03880) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P03880
- Elsewhere: RCSB PDB 3EH8 · PDBe 3EH8 · UniProt P03880
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.