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 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
- 6FB2
- 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.-.-
- UniProt
- P05725
- Ligands
- MN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 153 | 51% helix, 20% strand | P05725 |
| B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 154 | 54% helix, 20% strand | P05725 |
| 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
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D, F, E, 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 | 221 | 0.77 | 0.91 | 36 | empty |
| 2 | 95 | 0.66 | 0.91 | 18 | empty |
| 3 | 58 | 0.32 | 0.77 | 16 | empty |
Interfaces
14 interfaces between chains.
- A–B · 989 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 839 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 781 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–G · 764 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–E · 729 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6FB2 · Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in… · the same entry in another collection · chain G against G, TM-score 1.00
- P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain A 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 6FB2 · PDBe 6FB2 · UniProt P05725
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