Research workbench
Crystal structure of a tailored I-crei homing endonuclease protein (3115 variant) in complex with its target DNA (haemoglobin beta subunit gene) in the presence of magnesium
Analyse Crystal structure of a tailored I-crei homing endonuclease protein (3115… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FB1
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA endonuclease I-crei; DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*CP*TP*CP*CP*AP*C)-3'); DNA…
- EC
- 3.1.-.-
- Ligands
- MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 153 | 50% helix, 20% strand | — |
| B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 154 | 53% helix, 20% strand | — |
| D | DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*CP*TP*CP*CP*AP*C)-3') | dna | 14 | — | — |
| F | DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*G)-3') | dna | 14 | — | — |
| E | DNA (5'-D(P*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3') | dna | 10 | — | — |
| G | DNA (5'-D(P*AP*GP*AP*AP*GP*TP*CP*TP*GP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, F, E, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.77 | 0.92 | 36 | empty |
| 2 | 113 | 0.70 | 0.92 | 20 | empty |
| 3 | 59 | 0.31 | 0.76 | 17 | empty |
Interfaces
14 interfaces between chains.
- A–B · 984 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 812 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–D · 780 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–E · 748 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–G · 741 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6FB1 · Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6FB1 · PDBe 6FB1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.