Research workbench
Hincii bound to CA2+ and cognate DNA gtcgac
Analyse Hincii bound to CA2+ and cognate DNA gtcgac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TW8
- Type
- protein + DNA
- Length
- 1,077 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'; Hinc II endonuclease
- EC
- 3.1.21.4
- UniProt
- E1B6R0
- Ligands
- CA, NA
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3' | dna | 13 | — | — |
| A, C | Hinc II endonuclease (EC 3.1.21.4) | protein | 257 | 45% helix, 21% strand | E1B6R0 |
| B | Hinc II endonuclease (EC 3.1.21.4) | protein | 256 | 41% helix, 20% strand | E1B6R0 |
| D | Hinc II endonuclease (EC 3.1.21.4) | protein | 255 | 41% helix, 21% strand | E1B6R0 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains E, F, H, A, B, C, G, D
- NA · Sodium ion · metal · 4 copies · chains F, A, E, B, H, C, G, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.82 | 0.84 | 77 | empty |
| 2 | 462 | 0.73 | 0.82 | 56 | empty |
| 3 | 276 | 0.65 | 0.83 | 23 | empty |
| 4 | 284 | 0.65 | 0.82 | 23 | empty |
| 5 | 480 | 0.65 | 0.77 | 34 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1826 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1728 Ų buried · 12 hydrogen bonds · protein-protein
- E–B · 1018 Ų buried · 24 hydrogen bonds · protein-nucleic
- H–C · 1009 Ų buried · 21 hydrogen bonds · protein-nucleic
- G–D · 1005 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 1TW8 · HincII bound to Ca2+ and cognate DNA GTCGAC · the same entry in another collection · chain E against E, 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 E1B6R0
- Elsewhere: RCSB PDB 1TW8 · PDBe 1TW8 · UniProt E1B6R0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.