MolNFT v1 · #3225 · protein + DNA
A pre-transition state eco ri ENDONUCLEASE/COGNATE DNA (tcgcgapttcgcg) complex with DNA base analog purine (P)
1CL8 · DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN) P*TP*TP*CP*GP*CP*G)-3'): “A pre-transition state eco ri ENDONUCLEASE/COGNATE DNA (tcgcgapttcgcg) complex with DNA base analog purine (P)”. X-ray diffraction, 3 pockets (best druggability 0.39).…
- PDB
- 1CL8
- Type
- protein + DNA
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN) P*TP*TP*CP*GP*CP*G)-3'); Protein (endonuclease)
- UniProt
- P00642
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN) P*TP*TP*CP*GP*CP*G)-3') | dna | 13 | — | — |
| A | Protein (endonuclease) | protein | 261 | 35% helix, 20% strand | P00642 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.39 | 0.74 | 17 | empty |
| 2 | 67 | 0.32 | 0.75 | 15 | empty |
| 3 | 62 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 796 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1CL8 · A pre-transition state eco ri ENDONUCLEASE/COGNATE DNA (tcgcgapttcgcg) complex with DNA… · the same entry in another collection · chain B against B, TM-score 1.00
- P00642 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecori (P00642) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00642
- Elsewhere: RCSB PDB 1CL8 · PDBe 1CL8 · UniProt P00642
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