MolNFT v1 · #158459 · protein + DNA
Non-covalent DNA-protein complex between E. COLI yedk and ssdna containing an abasic site analog
6NUH · Sos response-associated peptidase yedk: “Non-covalent DNA-protein complex between E. COLI yedk and ssdna containing an abasic site analog”. X-ray diffraction, 1 ligand (PDI), 1 pocket (best druggability 0.34). MolNFT v1 #158459 on…
- PDB
- 6NUH
- Type
- protein + DNA
- Length
- 232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sos response-associated peptidase yedk; DNA (5'-D(*GP*TP*CP*(PDI)P*GP*GP*A)-3')
- EC
- 3.4.-.-
- UniProt
- P76318
- Ligands
- PDI
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sos response-associated peptidase yedk (EC 3.4.-.-) | protein | 226 | 24% helix, 35% strand | P76318 |
| C | DNA (5'-D(*GP*TP*CP*(PDI)P*GP*GP*A)-3') | dna | 6 | — | — |
Ligands and binding sites
- PDI · Phosphoric acid mono-(3-hydroxy-propyl) ester · ligand · chains A, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.34 | 0.78 | 14 | PDI |
Interfaces
1 interface between chains.
- A–C · 863 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6NUH · Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site… · the same entry in another collection · chain A against A, TM-score 1.00
- P76318 · AlphaFold monomer V2.0 prediction for abasic site processing protein yedk (P76318) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P76318
- Elsewhere: RCSB PDB 6NUH · PDBe 6NUH · UniProt P76318
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