Research workbench
Crystal structure of a tailored I-crei homing endonuclease protein (3115 variant) in complex with an altered version of its target DNA (haemoglobin beta subunit gene) at 5NNN region in the presence of manganese
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
- 6FB6
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-crei monomer a; I-crei monomer B; DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*C)-3…
- Ligands
- MN
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-crei monomer a | protein | 153 | 52% helix, 21% strand | — |
| B | I-crei monomer B | protein | 154 | 56% helix, 20% strand | — |
| D | DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*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*GP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3') | dna | 10 | — | — |
| G | DNA (5'-D(P*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D, G, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.68 | 0.94 | 14 | empty |
| 2 | 117 | 0.67 | 0.90 | 25 | empty |
| 3 | 68 | 0.45 | 0.83 | 19 | empty |
| 4 | 65 | 0.42 | 0.82 | 18 | empty |
| 5 | 59 | 0.40 | 0.81 | 19 | empty |
Interfaces
15 interfaces between chains.
- A–B · 952 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 904 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 870 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–E · 753 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–G · 741 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 6FB6 · 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 6FB6 · PDBe 6FB6
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