MolNFT v1 · #113608 · protein + DNA
The crystal structure of I-dmoi G20S in complex with its target DNA in the presence of 2MM mg
5AKM · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi G20S in complex with its target DNA in the presence of 2MM mg”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.54). MolNFT v1 #113608 on GenesisL1: 3D…
- PDB
- 5AKM
- Type
- protein + DNA
- Length
- 685 residues
- Chains
- 15
- 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
- MG
- Pockets
- 14 · best druggability 0.54
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 183 | 48% 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, H, M | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' | dna | 11 | — | — |
| D, I, N | 5'-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 | 174 | 51% helix, 26% strand | P21505 |
| K | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 178 | 51% helix, 26% strand | P21505 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E, F, G, J, H, I, K, L, N, O
- ACT · Acetate ion · additive · 3 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.54 | 0.76 | 26 | empty |
| 2 | 266 | 0.52 | 0.75 | 29 | empty |
| 3 | 279 | 0.52 | 0.75 | 26 | empty |
| 4 | 170 | 0.43 | 0.74 | 27 | empty |
| 5 | 90 | 0.40 | 0.78 | 19 | empty |
Interfaces
33 interfaces between chains.
- F–I · 1072 Ų buried · 26 hydrogen bonds · protein-nucleic
- K–N · 1034 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–D · 936 Ų buried · 23 hydrogen bonds · protein-nucleic
- F–G · 823 Ų buried · 22 hydrogen bonds · protein-nucleic
- K–L · 783 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 5AKM · The crystal structure of I-dmoi G20S in complex with its target DNA in the presence of… · 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 5AKM · PDBe 5AKM · UniProt P21505
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