Research workbench
Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA at 2.0 ångström resolution
Analyse Crystal structural analysis of hindiii restriction endonuclease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E52
- Type
- protein + DNA
- Length
- 1,266 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II restriction enzyme hindiii; DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP…
- EC
- 3.1.21.4
- UniProt
- P43870
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Type II restriction enzyme hindiii (EC 3.1.21.4) | protein | 299 | 59% helix, 12% strand | P43870 |
| B, D | Type II restriction enzyme hindiii (EC 3.1.21.4) | protein | 298 | 58% helix, 11% strand | P43870 |
| E, F, G, H, I, J | DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)- 3') | dna | 12 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, E, G, C, D
- ACT · Acetate ion · additive · 3 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.79 | 0.83 | 63 | empty |
| 2 | 852 | 0.78 | 0.81 | 57 | empty |
| 3 | 512 | 0.71 | 0.81 | 64 | empty |
| 4 | 137 | 0.69 | 0.90 | 24 | empty |
| 5 | 267 | 0.67 | 0.83 | 42 | ACT |
Interfaces
17 interfaces between chains.
- C–D · 3490 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3461 Ų buried · 31 hydrogen bonds · protein-protein
- A–G · 838 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–H · 836 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–F · 831 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 2E52 · Crystal structural analysis of HindIII restriction endonuclease in complex with cognate… · the same entry in another collection · chain J against J, TM-score 1.00
- P43870 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme hindiii (P43870) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P43870
- Elsewhere: RCSB PDB 2E52 · PDBe 2E52 · UniProt P43870
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