MolNFT v1 · #113609 · protein + DNA
The crystal structure of I-dmoi Q42AK120M in complex with its target DNA nicked in the non-coding strand B and in the presence of 2MM mn
5AKN · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi Q42AK120M in complex with its target DNA nicked in the non-coding strand B…”. X-ray diffraction, 1 ligand (MN), 9 pockets (best druggability 0.59). MolNFT v1 #113609 on…
- PDB
- 5AKN
- Type
- protein + DNA
- Length
- 695 residues
- Chains
- 13
- 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
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 8 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 178 | 50% helix, 25% strand | P21505 |
| B, G, L | 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' | dna | 14 | — | — |
| C | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3 | dna | 11 | — | — |
| D | D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' | dna | 15 | — | — |
| E, J, O | 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' | dna | 10 | — | — |
| F | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 184 | 46% helix, 25% strand | P21505 |
| H, M | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP*CP*GP*CP *GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3' | dna | 26 | — | — |
| K | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 183 | 48% helix, 25% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, E, C, D, F, G, J, H, K, M, L, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.59 | 0.79 | 42 | empty |
| 2 | 241 | 0.50 | 0.75 | 29 | empty |
| 3 | 150 | 0.49 | 0.78 | 20 | empty |
| 4 | 89 | 0.43 | 0.79 | 27 | MN |
| 5 | 157 | 0.41 | 0.74 | 24 | empty |
Interfaces
23 interfaces between chains.
- K–M · 1416 Ų buried · 37 hydrogen bonds · protein-nucleic
- F–H · 1409 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–D · 998 Ų buried · 26 hydrogen bonds · protein-nucleic
- F–G · 795 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 790 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 5AKN · THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE… · the same entry in another collection · chain O against O, 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 5AKN · PDBe 5AKN · UniProt P21505
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