MolNFT v1 · #52146 · protein + DNA
The crystal structure of I-dmoi in complex with DNA and mn
2VS8 · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi in complex with DNA and mn”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.54). MolNFT v1 #52146 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VS8
- Type
- protein + DNA
- Length
- 701 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*A)-3'…
- EC
- 3.1.-.-
- UniProt
- P21505
- Ligands
- MN
- Pockets
- 13 · best druggability 0.54
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 183 | 44% helix, 25% strand | P21505 |
| B, G, L | 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*A)-3' | dna | 14 | — | — |
| C, H, M | 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP* DGP*DCP*DGP)-3' | dna | 11 | — | — |
| D, I, N | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*C)-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 | 191 | 49% helix, 24% strand | P21505 |
| K | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 177 | 49% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, E, C, D, F, H, I, G, J, K, L, O, M, N
- 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
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.54 | 0.76 | 27 | empty |
| 2 | 259 | 0.52 | 0.76 | 27 | empty |
| 3 | 137 | 0.50 | 0.79 | 25 | ACT |
| 4 | 130 | 0.42 | 0.76 | 23 | empty |
| 5 | 99 | 0.42 | 0.77 | 18 | ACT |
Interfaces
36 interfaces between chains.
- F–I · 1059 Ų buried · 24 hydrogen bonds · protein-nucleic
- K–N · 1021 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–D · 1010 Ų buried · 26 hydrogen bonds · protein-nucleic
- F–G · 811 Ų buried · 23 hydrogen bonds · protein-nucleic
- K–L · 791 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 2VS8 · The crystal structure of I-DmoI in complex with DNA and Mn · 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 2VS8 · PDBe 2VS8 · UniProt P21505
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