Research workbench
Crystal structure of the ternary ecorv-DNA-lu complex with cleaved DNA substrate.
Analyse Crystal structure of the ternary ecorv-DNA-lu complex with cleaved DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HLK
- Type
- protein + DNA
- Length
- 511 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme ecorv; DNA (5'-D(*AP*AP*AP*GP*AP*TP)-3'); DNA…
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- NA, LU
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type-2 restriction enzyme ecorv (EC 3.1.21.4) | protein | 244 | 34% helix, 29% strand | P04390 |
| C, D | DNA (5'-D(*AP*AP*AP*GP*AP*TP)-3') | dna | 6 | — | — |
| E | DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3') | dna | 5 | — | — |
| F | DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3') | dna | 6 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D
- LU · Lutetium (III) ion · metal · 4 copies · chains A, B, E, F, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.84 | 0.92 | 61 | LU |
| 2 | 192 | 0.58 | 0.81 | 27 | empty |
| 3 | 176 | 0.58 | 0.81 | 28 | empty |
| 4 | 239 | 0.54 | 0.77 | 37 | EDO |
| 5 | 80 | 0.38 | 0.78 | 13 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2207 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 483 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–E · 440 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 354 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 328 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5HLK · Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate. · the same entry in another collection · chain A against A, 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 5HLK · PDBe 5HLK · UniProt P04390
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