MolNFT v1 · #27372 · protein + DNA
Hincii bound to cleaved, cognate DNA containing gtcgac
1XHU · 5'-D(*GP*CP*CP*GP*GP*TP*C)-3': “Hincii bound to cleaved, cognate DNA containing gtcgac”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #27372 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XHU
- Type
- protein + DNA
- Length
- 1,075 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*CP*GP*GP*TP*C)-3'; 5'-D(P*GP*AP*CP*CP*GP*G)-3'; Type II restriction enzyme…
- EC
- 3.1.21.4
- UniProt
- P17743
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G, I, K | 5'-D(*GP*CP*CP*GP*GP*TP*C)-3' | dna | 7 | — | — |
| F, H, J, L | 5'-D(P*GP*AP*CP*CP*GP*G)-3' | dna | 6 | — | — |
| A | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 257 | 41% helix, 21% strand | P17743 |
| B, D | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 256 | 38% helix, 22% strand | P17743 |
| C | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 254 | 38% helix, 19% strand | P17743 |
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.81 | 0.85 | 71 | empty |
| 2 | 337 | 0.67 | 0.82 | 26 | empty |
| 3 | 311 | 0.67 | 0.82 | 25 | empty |
| 4 | 415 | 0.63 | 0.78 | 43 | empty |
| 5 | 405 | 0.63 | 0.78 | 64 | empty |
Interfaces
33 interfaces between chains.
- A–B · 1789 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1745 Ų buried · 10 hydrogen bonds · protein-protein
- J–D · 692 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–B · 691 Ų buried · 17 hydrogen bonds · protein-nucleic
- L–C · 671 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 1XHU · HincII bound to cleaved, cognate DNA containing GTCGAC · the same entry in another collection · chain B against B, 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 P17743
- Elsewhere: RCSB PDB 1XHU · PDBe 1XHU · UniProt P17743
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