Research workbench
Crystal structure of paci-DNA enzyme product complex
Analyse Crystal structure of paci-DNA enzyme product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M7K
- Type
- protein + DNA
- Length
- 160 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease paci; DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3'); DNA…
- Ligands
- NA, ZN, MG, PT, SO4
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease paci | protein | 142 | 42% helix, 14% strand | — |
| B | DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3') | dna | 10 | — | — |
| C | DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 9 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A, C
- PT · Platinum (II) ion · metal · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.53 | 0.82 | 13 | empty |
| 2 | 102 | 0.36 | 0.75 | 17 | MG |
Interfaces
3 interfaces between chains.
- A–C · 860 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 637 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 329 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Compared structures
- 3M7K · Crystal structure of PacI-DNA Enzyme product complex · 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
- Elsewhere: RCSB PDB 3M7K · PDBe 3M7K
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