MolNFT v1 · #121178 · protein + DNA
Crystal structure of T5FEN in complex intact substrate and metal ions.
5HNK · DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3'): “Crystal structure of T5FEN in complex intact substrate and metal ions.”. X-ray diffraction, 2 ligands (MG, K), 4 pockets (best druggability 0.85). MolNFT v1 #121178 on GenesisL1…
- PDB
- 5HNK
- Type
- protein + DNA
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3'); Exodeoxyribonuclease
- EC
- 3.1.11.3
- UniProt
- P06229
- Ligands
- MG, K
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3') | dna | 12 | — | — |
| A, B | Exodeoxyribonuclease (EC 3.1.11.3) | protein | 272 | 61% helix, 11% strand | P06229 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains Y, B
- K · Potassium ion · metal · chains Y, A
- GOL · Glycerol · additive · chains Y, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.85 | 0.87 | 116 | MG |
| 2 | 295 | 0.64 | 0.81 | 42 | empty |
| 3 | 62 | 0.58 | 0.90 | 22 | empty |
| 4 | 182 | 0.52 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- Y–B · 800 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 506 Ų buried · 10 hydrogen bonds · protein-protein
- X–B · 499 Ų buried · 8 hydrogen bonds · protein-nucleic
- X–A · 440 Ų buried · 7 hydrogen bonds · protein-nucleic
- X–Y · 381 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 5HNK · Crystal structure of T5Fen in complex intact substrate and metal ions. · the same entry in another collection · chain X against X, 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 P06229
- Elsewhere: RCSB PDB 5HNK · PDBe 5HNK · UniProt P06229
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