Research workbench
Tetrameric restriction endonuclease ngomiv in complex with cleaved DNA
Analyse Tetrameric restriction endonuclease ngomiv in complex with cleaved DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FIU
- Type
- protein + DNA
- Length
- 1,188 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*CP*G)-3'); DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3'); Type II restriction…
- EC
- 3.1.21.4
- UniProt
- P31032
- Ligands
- MG
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | DNA (5'-D(*TP*GP*CP*G)-3') | dna | 4 | — | — |
| I, J, K, L | DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3') | dna | 7 | — | — |
| A, B, C, D | Type II restriction enzyme ngomi (EC 3.1.21.4) | protein | 286 | 46% helix, 13% strand | P31032 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains E, I, B, F, J, A, G, K, C, L, D
- ACY · Acetic acid · additive · 4 copies · chains J, A, I, B, K, C, L, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.88 | 0.89 | 126 | empty |
| 2 | 593 | 0.78 | 0.84 | 60 | MG |
| 3 | 584 | 0.76 | 0.83 | 60 | empty |
| 4 | 663 | 0.76 | 0.82 | 56 | empty |
| 5 | 61 | 0.73 | 0.99 | 25 | empty |
Interfaces
32 interfaces between chains.
- A–D · 2967 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 2950 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 1045 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 970 Ų buried · 5 hydrogen bonds · protein-protein
- L–D · 560 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1FIU · Tetrameric restriction endonuclease ngomiv in complex with cleaved DNA · the same entry in another collection · chain D against D, 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
- Every structure of UniProt P31032
- Elsewhere: RCSB PDB 1FIU · PDBe 1FIU · UniProt P31032
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