MolNFT v1 · #148586 · protein + DNA
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 calcium
6FB0 · DNA endonuclease I-crei: “Crystal structure of a tailored I-crei homing endonuclease protein (3115 variant) in complex with its target…”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.71). MolNFT v1 #148586 on…
- PDB
- 6FB0
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 4
- 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*CP*AP*GP*GP*AP…
- EC
- 3.1.-.-
- Ligands
- CA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 153 | 55% helix, 21% strand | — |
| B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 154 | 53% helix, 21% strand | — |
| D | DNA (5'- D(*TP*CP*AP*GP*AP*CP*TP*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP* GP*A)-3') | dna | 24 | — | — |
| F | DNA (5'- D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*AP*AP*GP*TP*CP*TP* GP*A)-3') | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, D, F
- ACT · Acetate ion · additive · 5 copies · chains A, B, F
- PGO · S-1,2-propanediol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.71 | 0.92 | 36 | empty |
| 2 | 97 | 0.69 | 0.92 | 19 | empty |
| 3 | 66 | 0.50 | 0.86 | 21 | ACT |
| 4 | 68 | 0.47 | 0.83 | 21 | PGO |
| 5 | 70 | 0.38 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–F · 1150 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- A–B · 959 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 897 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–F · 887 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–F · 862 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6FB0 · 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 6FB0 · PDBe 6FB0
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