MolNFT v1 · #62052 · protein + DNA
Q138F hincii bound to gttaac and cocrystallized with 5 mm CA2+
3E40 · Type-2 restriction enzyme hindii: “Q138F hincii bound to gttaac and cocrystallized with 5 mm CA2+”. X-ray diffraction, 2 ligands (NA, CA), 10 pockets (best druggability 0.68). MolNFT v1 #62052 on GenesisL1: 3D structure, binding…
- PDB
- 3E40
- Type
- protein + DNA
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme hindii; 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DP*DAP*DAP*DCP*DCP*DGP*DGP…
- EC
- 3.1.21.4
- UniProt
- P44413
- Ligands
- NA, CA
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-2 restriction enzyme hindii (EC 3.1.21.4) | protein | 247 | 43% helix, 23% strand | P44413 |
| B | Type-2 restriction enzyme hindii (EC 3.1.21.4) | protein | 241 | 43% helix, 24% strand | P44413 |
| E, F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DP*DAP*DAP*DCP*DCP*DGP*DGP*DC )-3') | dna | 14 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, F, B, E
- CA · Calcium ion · metal · 2 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.68 | 0.81 | 28 | empty |
| 2 | 393 | 0.68 | 0.81 | 27 | empty |
| 3 | 155 | 0.46 | 0.76 | 16 | empty |
| 4 | 148 | 0.44 | 0.76 | 21 | empty |
| 5 | 114 | 0.44 | 0.78 | 18 | NA |
Interfaces
6 interfaces between chains.
- A–B · 1280 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 897 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–E · 843 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–F · 650 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–E · 613 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 3E40 · Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+ · the same entry in another collection · chain A against A, TM-score 1.00
- P44413 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme hindii (P44413) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3E40 · PDBe 3E40 · UniProt P44413
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