MolNFT v1 · #107982 · protein + DNA
The crystal structure of I-dmoi in complex with its target DNA at 10 days incubation in 5MM mn (state 7)
4UT0 · Homing endonuclease I-dmoi: “The crystal structure of I-dmoi in complex with its target DNA at 10 days incubation in 5MM mn (state 7)”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.55). MolNFT v1 #107982 on…
- PDB
- 4UT0
- Type
- protein + DNA
- Length
- 702 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
- MN
- Pockets
- 13 · best druggability 0.55
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 25% 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 | 191 | 50% helix, 24% strand | P21505 |
| K | Homing endonuclease I-dmoi (EC 3.1.-.-) | protein | 178 | 49% helix, 26% strand | P21505 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, E, C, D, F, G, J, H, I, K, M, N, L, 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
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.55 | 0.76 | 27 | empty |
| 2 | 137 | 0.53 | 0.81 | 26 | ACT |
| 3 | 252 | 0.52 | 0.76 | 28 | empty |
| 4 | 137 | 0.48 | 0.77 | 23 | ACT |
| 5 | 187 | 0.43 | 0.74 | 30 | empty |
Interfaces
33 interfaces between chains.
- F–I · 1045 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–D · 991 Ų buried · 26 hydrogen bonds · protein-nucleic
- K–N · 983 Ų buried · 28 hydrogen bonds · protein-nucleic
- F–G · 812 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 787 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 4UT0 · The crystal structure of I-dmoi in complex with its target DNA at 10 days incubation in… · 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 4UT0 · PDBe 4UT0 · UniProt P21505
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