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The crystal structure of I-dmoi Q42AK120M in complex with its target DNA in the presence of 2MM mn
Analyse The crystal structure of I-dmoi Q42AK120M in complex with its target DNA in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AK9
- Type
- protein + DNA
- Length
- 698 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
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 183 | 49% helix, 26% strand | P21505 |
| B, F, K | 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3' | dna | 14 | — | — |
| C, G, L | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3 | dna | 11 | — | — |
| D, H, N | 25MER | dna | 25 | — | — |
| J | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 182 | 49% helix, 25% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, D, C, E, F, H, G, J, K, N, L
- ACT · Acetate ion · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.71 | 0.77 | 54 | empty |
| 2 | 223 | 0.53 | 0.78 | 26 | empty |
| 3 | 188 | 0.52 | 0.78 | 26 | empty |
| 4 | 143 | 0.44 | 0.76 | 24 | empty |
| 5 | 172 | 0.43 | 0.74 | 26 | empty |
Interfaces
21 interfaces between chains.
- E–H · 1298 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–D · 1297 Ų buried · 34 hydrogen bonds · protein-nucleic
- J–N · 1279 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 797 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–F · 786 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 5AK9 · The crystal structure of I-dmoi Q42AK120M in complex with its target DNA in the presence… · the same entry in another collection · chain N against N, 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 5AK9 · PDBe 5AK9 · UniProt P21505
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