Research workbench
Expanding lagalidadg endonuclease scaffold diversity by rapidly surveying evolutionary sequence space
Analyse Expanding lagalidadg endonuclease scaffold diversity by rapidly surveying… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UVF
- Type
- protein + DNA
- Length
- 622 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intron-encoded DNA endonuclease I-hjemi; Synthetic oligo
- EC
- 3.1.-.-
- Ligands
- CA, NA, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Intron-encoded DNA endonuclease I-hjemi (EC 3.1.-.-) | protein | 255 | 43% helix, 22% strand | — |
| C, E | Synthetic oligo | dna | 28 | — | — |
| D, F | Synthetic oligo | dna | 28 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C, D, B, E, F
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.75 | 0.79 | 61 | empty |
| 2 | 59 | 0.67 | 0.96 | 22 | empty |
| 3 | 430 | 0.66 | 0.79 | 52 | CA |
| 4 | 387 | 0.58 | 0.76 | 37 | empty |
| 5 | 267 | 0.56 | 0.78 | 40 | CA |
Interfaces
9 interfaces between chains.
- B–E · 1490 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–C · 1428 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–F · 1387 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–D · 1377 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–F · 1353 Ų buried · 130 hydrogen bonds · nucleic-nucleic
Compared structures
- 3UVF · Expanding LAGALIDADG endonuclease scaffold diversity by rapidly surveying evolutionary… · 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 3UVF · PDBe 3UVF
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