Research workbench
Structure of recj complexed with dtmp
Analyse Structure of recj complexed with dtmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F54
- Type
- protein
- Length
- 693 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded-DNA-specific exonuclease
- UniProt
- D0EM60
- Ligands
- TMP, MN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded-DNA-specific exonuclease | protein | 693 | 46% helix, 17% strand | D0EM60 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.76 | 0.79 | 91 | TMP |
| 2 | 67 | 0.46 | 0.83 | 15 | empty |
| 3 | 106 | 0.37 | 0.74 | 17 | empty |
| 4 | 64 | 0.36 | 0.78 | 20 | empty |
| 5 | 79 | 0.34 | 0.75 | 16 | empty |
Compared structures
- 5F54 · Structure of RecJ complexed with dTMP · 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 5F54 · PDBe 5F54 · UniProt D0EM60
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