MolNFT v1 · #156044 · protein + DNA
Structure of recj complexed with a 5'-P-dspacer-modified ssdna
6LRD · Single-stranded-DNA-specific exonuclease: “Structure of recj complexed with a 5'-P-dspacer-modified ssdna”. X-ray diffraction, 2 ligands (MN, SO4), 8 pockets (best druggability 0.59). MolNFT v1 #156044 on GenesisL1: 3D structure…
- PDB
- 6LRD
- Type
- protein + DNA
- Length
- 708 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded-DNA-specific exonuclease; DNA (5'-D(P*(3DR)P*TP*TP*TP*TP*T)-3')…
- UniProt
- D0EM60
- Ligands
- MN, SO4
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded-DNA-specific exonuclease | protein | 698 | 47% helix, 17% strand | D0EM60 |
| C | DNA (5'-D(P*(3DR)P*TP*TP*TP*TP*T)-3') | dna | 6 | — | — |
| B | Asp-leu-pro-phe | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.59 | 0.76 | 45 | empty |
| 2 | 81 | 0.45 | 0.81 | 16 | empty |
| 3 | 171 | 0.45 | 0.74 | 33 | empty |
| 4 | 120 | 0.44 | 0.78 | 23 | SO4 |
| 5 | 101 | 0.43 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1220 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–B · 334 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6LRD · Structure of RecJ complexed with a 5'-P-dSpacer-modified ssDNA · 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 D0EM60
- Elsewhere: RCSB PDB 6LRD · PDBe 6LRD · UniProt D0EM60
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