Research workbench
Crystal structure of type iif restriction endonuclease ngomiv with cognate uncleaved DNA
Analyse Crystal structure of type iif restriction endonuclease ngomiv with cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ABT
- Type
- protein + DNA
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme ngomiv; 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
- EC
- 3.1.21.4
- UniProt
- P31032
- Ligands
- CA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type-2 restriction enzyme ngomiv (EC 3.1.21.4) | protein | 286 | 46% helix, 14% strand | P31032 |
| E, G | 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3' | dna | 11 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, E, B, G
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 | 59 | 0.66 | 0.95 | 24 | empty |
| 2 | 99 | 0.57 | 0.86 | 28 | empty |
| 3 | 118 | 0.45 | 0.78 | 20 | empty |
| 4 | 106 | 0.44 | 0.79 | 16 | empty |
| 5 | 58 | 0.26 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2994 Ų buried · 72 hydrogen bonds · protein-protein
- A–E · 773 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–G · 764 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 4ABT · Crystal structure of Type IIF restriction endonuclease NgoMIV with cognate uncleaved DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P31032 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ngomiv (P31032) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P31032
- Elsewhere: RCSB PDB 4ABT · PDBe 4ABT · UniProt P31032
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