MolNFT v1 · #118643 · protein + DNA
Crystal structure of the ternary ecorv-DNA-lu complex with uncleaved DNA substrate. lanthanide binding to ecorv-DNA complex inhibits cleavage.
5F8A · DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*T)-3'): “Crystal structure of the ternary ecorv-DNA-lu complex with uncleaved DNA substrate. lanthanide binding to…”. X-ray diffraction, 2 ligands (LU, NA), 7 pockets (best druggability…
- PDB
- 5F8A
- Type
- protein + DNA
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*T)-3'); Type-2 restriction enzyme ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- LU, NA
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*T)-3') | dna | 12 | — | — |
| A, B | Type-2 restriction enzyme ecorv (EC 3.1.21.4) | protein | 244 | 34% helix, 29% strand | P04390 |
Ligands and binding sites
- LU · Lutetium (III) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.76 | 0.90 | 49 | LU |
| 2 | 205 | 0.71 | 0.88 | 38 | LU |
| 3 | 196 | 0.57 | 0.80 | 29 | empty |
| 4 | 146 | 0.55 | 0.82 | 27 | empty |
| 5 | 197 | 0.53 | 0.78 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2215 Ų buried · 30 hydrogen bonds · protein-protein
- C–A · 754 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–B · 738 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–B · 559 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 527 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5F8A · Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate.… · the same entry in another collection · chain C against C, TM-score 1.00
- P04390 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecorv (P04390) · a predicted model of the same protein · 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 P04390
- Elsewhere: RCSB PDB 5F8A · PDBe 5F8A · UniProt P04390
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