MolNFT v1 · #27373 · protein + DNA
Hincii bound to cleaved cognate DNA gtcgac and MN2+
1XHV · 5'-D(*GP*CP*CP*GP*GP*TP*C)-3': “Hincii bound to cleaved cognate DNA gtcgac and MN2+”. X-ray diffraction, 1 ligand (MN), 12 pockets (best druggability 0.82). MolNFT v1 #27373 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1XHV
- Type
- protein + DNA
- Length
- 1,052 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
- Ligands
- MN
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 22% 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 | 254 | 43% helix, 22% strand | P17743 |
| B | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 252 | 40% helix, 23% strand | P17743 |
| C | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 247 | 43% helix, 21% strand | P17743 |
| D | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 247 | 41% helix, 22% strand | P17743 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 22 copies · chains E, F, B, G, H, A, J, D, L, C, K, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.82 | 0.85 | 70 | empty |
| 2 | 780 | 0.73 | 0.78 | 57 | MN |
| 3 | 861 | 0.69 | 0.75 | 61 | MN |
| 4 | 329 | 0.68 | 0.83 | 23 | empty |
| 5 | 312 | 0.68 | 0.83 | 24 | empty |
Interfaces
34 interfaces between chains.
- A–B · 1592 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1333 Ų buried · 8 hydrogen bonds · protein-protein
- F–B · 658 Ų buried · 14 hydrogen bonds · protein-nucleic
- H–A · 569 Ų buried · 15 hydrogen bonds · protein-nucleic
- J–D · 553 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 1XHV · HincII bound to cleaved cognate DNA GTCGAC and Mn2+ · 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 P17743
- Elsewhere: RCSB PDB 1XHV · PDBe 1XHV · UniProt P17743
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