MolNFT v1 · #65163 · protein + DNA
Crystal structure of the beta-beta-alpha-me type II restriction endonuclease HPY99I in the absence of edta
3GOX: “Crystal structure of the beta-beta-alpha-me type II restriction endonuclease HPY99I in the absence of edta”. X-ray diffraction, 2 ligands (ZN, NA), 6 pockets (best druggability 0.61). MolNFT v1 #65163 on GenesisL1: 3D structure…
- PDB
- 3GOX
- Type
- protein + DNA
- Length
- 398 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease HPY99I; 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'…
- UniProt
- Q9ZL26
- Ligands
- ZN, NA
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Restriction endonuclease HPY99I | protein | 189 | 25% helix, 33% strand | Q9ZL26 |
| C | 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3' | dna | 10 | — | — |
| D | 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3' | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, D, B, C
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.61 | 0.78 | 42 | empty |
| 2 | 329 | 0.61 | 0.78 | 36 | empty |
| 3 | 136 | 0.47 | 0.79 | 17 | empty |
| 4 | 83 | 0.42 | 0.79 | 16 | empty |
| 5 | 114 | 0.41 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2822 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 841 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 833 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–D · 467 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 454 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 3GOX · Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in… · the same entry in another collection · chain A against A, 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 Q9ZL26
- Elsewhere: RCSB PDB 3GOX · PDBe 3GOX · UniProt Q9ZL26
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