MolNFT v1 · #113601 · protein + DNA
The crystal structure of I-dmoi Q42AK120M in complex with its target DNA nicked in the coding strand a and in the presence of 2MM mn
5AKF · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi Q42AK120M in complex with its target DNA nicked in the coding strand a and in…”. X-ray diffraction, 2 ligands (MN, CL), 10 pockets (best druggability 0.62). MolNFT v1…
- PDB
- 5AKF
- Type
- protein + DNA
- Length
- 680 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homing endonuclease I-dmoi; 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'…
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN, CL
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 179 | 50% helix, 25% strand | P21505 |
| B, F, J | 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' | dna | 14 | — | — |
| C, G, K | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' | dna | 11 | — | — |
| D, H, L | 25MER | dna | 25 | — | — |
| E | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 176 | 51% helix, 27% strand | P21505 |
| I | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 175 | 50% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D, E, F, H, I, J, L
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E, I
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.62 | 0.77 | 50 | ACT |
| 2 | 134 | 0.45 | 0.77 | 25 | empty |
| 3 | 107 | 0.42 | 0.78 | 13 | empty |
| 4 | 113 | 0.41 | 0.77 | 23 | empty |
| 5 | 144 | 0.40 | 0.74 | 22 | empty |
Interfaces
21 interfaces between chains.
- E–H · 1296 Ų buried · 34 hydrogen bonds · protein-nucleic
- I–L · 1291 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–D · 1276 Ų buried · 34 hydrogen bonds · protein-nucleic
- E–F · 799 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 787 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 5AKF · The crystal structure of I-dmoi Q42AK120M in complex with its target DNA nicked in the… · the same entry in another collection · chain L against L, 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 P21505
- Elsewhere: RCSB PDB 5AKF · PDBe 5AKF · UniProt P21505
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.