MolNFT v1 · #12284 · protein + DNA
Hincii bound to cognate DNA
1KC6 · 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3': “Hincii bound to cognate DNA”. X-ray diffraction, 1 ligand (NA), 15 pockets (best druggability 0.74). MolNFT v1 #12284 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KC6
- Type
- protein + DNA
- Length
- 1,013 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3'; Type II restriction enzyme hincii
- EC
- 3.1.21.4
- UniProt
- P17743
- Ligands
- NA
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3' | dna | 12 | — | — |
| A | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 249 | 44% helix, 24% strand | P17743 |
| B | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 247 | 44% helix, 23% strand | P17743 |
| C | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 233 | 42% helix, 23% strand | P17743 |
| D | Type II restriction enzyme hincii (EC 3.1.21.4) | protein | 236 | 43% helix, 20% strand | P17743 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains F, A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.74 | 0.84 | 31 | empty |
| 2 | 416 | 0.73 | 0.84 | 30 | empty |
| 3 | 829 | 0.70 | 0.76 | 57 | empty |
| 4 | 384 | 0.67 | 0.81 | 27 | empty |
| 5 | 411 | 0.67 | 0.80 | 30 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1344 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1273 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 934 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–A · 901 Ų buried · 20 hydrogen bonds · protein-nucleic
- G–D · 888 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
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 1KC6 · PDBe 1KC6 · UniProt P17743
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