MolNFT v1 · #59056 · protein + DNA
Restriction endonuclease pspgi-substrate DNA complex
3BM3 · DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3'): “Restriction endonuclease pspgi-substrate DNA complex”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #59056 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3BM3
- Type
- protein + DNA
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3'); DNA…
- UniProt
- O93646
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3') | dna | 11 | — | — |
| D | DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3') | dna | 11 | — | — |
| A | Pspgi restriction endonuclease | protein | 259 | 56% helix, 11% strand | O93646 |
| B | Pspgi restriction endonuclease | protein | 258 | 56% helix, 10% strand | O93646 |
Ligands and binding sites
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.65 | 0.82 | 40 | empty |
| 2 | 68 | 0.47 | 0.84 | 17 | empty |
| 3 | 122 | 0.47 | 0.79 | 16 | empty |
| 4 | 59 | 0.36 | 0.78 | 14 | empty |
| 5 | 71 | 0.34 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1743 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 883 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 857 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–B · 688 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–A · 643 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3BM3 · Restriction endonuclease PspGI-substrate DNA complex · the same entry in another collection · chain C against C, 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 O93646
- Elsewhere: RCSB PDB 3BM3 · PDBe 3BM3 · UniProt O93646
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