MolNFT v1 · #13908 · protein + DNA
Crystal structure of E. COLI seqa complexed with hemimethylated DNA
1LRR · 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3': “Crystal structure of E. COLI seqa complexed with hemimethylated DNA”. X-ray diffraction, 4 pockets (best druggability 0.57). MolNFT v1 #13908 on GenesisL1: 3D structure, binding sites…
- PDB
- 1LRR
- Type
- protein + DNA
- Length
- 284 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'; 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G…
- UniProt
- P36658
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3' | dna | 12 | — | — |
| C, F | 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3' | dna | 12 | — | — |
| A, D | Seqa protein | protein | 118 | 60% helix, 7% strand | P36658 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.57 | 0.79 | 28 | empty |
| 2 | 51 | 0.24 | 0.73 | 12 | empty |
| 3 | 50 | 0.24 | 0.73 | 9 | empty |
| 4 | 50 | 0.23 | 0.72 | 14 | empty |
Interfaces
7 interfaces between chains.
- B–C · 562 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- E–F · 553 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- B–A · 457 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–A · 451 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 415 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1LRR · Crystal structure of E. COLI seqa complexed with hemimethylated DNA · 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
- Every structure of UniProt P36658
- Elsewhere: RCSB PDB 1LRR · PDBe 1LRR · UniProt P36658
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