Research workbench
Crystal structure of the I-crei homing endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of manganese
Analyse Crystal structure of the I-crei homing endonuclease D75N variant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FB9
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3'); DNA…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- MN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3') | dna | 14 | — | — |
| C | DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*TP*GP*CP*GP*TP*AP*C)-3') | dna | 14 | — | — |
| A | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 154 | 54% helix, 21% strand | P05725 |
| B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 153 | 53% helix, 21% strand | P05725 |
| F | DNA (5'-D(P*GP*CP*AP*GP*TP*TP*TP*TP*GP*A)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains E, A, B, D, C, F
- PGO · S-1,2-propanediol · additive · 4 copies · chains A, B, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.77 | 0.91 | 45 | empty |
| 2 | 149 | 0.75 | 0.93 | 30 | empty |
| 3 | 56 | 0.68 | 0.96 | 12 | empty |
| 4 | 55 | 0.41 | 0.81 | 13 | PGO |
| 5 | 56 | 0.40 | 0.81 | 17 | PGO |
Interfaces
15 interfaces between chains.
- A–B · 946 Ų buried · 16 hydrogen bonds · protein-protein
- C–A · 874 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–B · 846 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–F · 805 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 758 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6FB9 · Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an… · the same entry in another collection · chain D against D, TM-score 1.00
- P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P05725
- Elsewhere: RCSB PDB 6FB9 · PDBe 6FB9 · UniProt P05725
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