MolNFT v1 · #23335 · protein + DNA
Hincii bound to cognate DNA
1TX3 · 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3': “Hincii bound to cognate DNA”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.82). MolNFT v1 #23335 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1TX3
- Type
- protein + DNA
- Length
- 1,054 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'; Type II restriction enzyme hindii
- EC
- 3.1.21.4
- UniProt
- P44413
- Ligands
- NA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 22% 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 | Type II restriction enzyme hindii (EC 3.1.21.4) | protein | 249 | 40% helix, 23% strand | P44413 |
| B | Type II restriction enzyme hindii (EC 3.1.21.4) | protein | 254 | 41% helix, 22% strand | P44413 |
| C | Type II restriction enzyme hindii (EC 3.1.21.4) | protein | 255 | 38% helix, 22% strand | P44413 |
| D | Type II restriction enzyme hindii (EC 3.1.21.4) | protein | 244 | 41% helix, 20% strand | P44413 |
Ligands and binding sites
- 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
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.82 | 0.84 | 80 | empty |
| 2 | 1083 | 0.77 | 0.79 | 97 | empty |
| 3 | 916 | 0.76 | 0.79 | 76 | empty |
| 4 | 946 | 0.70 | 0.75 | 60 | empty |
| 5 | 363 | 0.67 | 0.82 | 25 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1514 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1389 Ų buried · 6 hydrogen bonds · protein-protein
- E–B · 999 Ų buried · 21 hydrogen bonds · protein-nucleic
- H–C · 994 Ų buried · 17 hydrogen bonds · protein-nucleic
- F–A · 905 Ų buried · 21 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 P44413
- Elsewhere: RCSB PDB 1TX3 · PDBe 1TX3 · UniProt P44413
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