MolNFT v1 · #114967 · protein + DNA
Poymerase nucleotide complex
5C5J · DNA polymerase IV: “Poymerase nucleotide complex”. X-ray diffraction, 2 ligands (8GT, MG), 7 pockets (best druggability 0.80). MolNFT v1 #114967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C5J
- Type
- protein + DNA
- Length
- 751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
- EC
- 2.7.7.7
- UniProt
- W8STT9
- Ligands
- 8GT, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 41% helix, 23% strand | W8STT9 |
| G, B | DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 18 | — | — |
| H | DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 14 | — | — |
| C | DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 17 | — | — |
Ligands and binding sites
- 8GT · 8-oxo-guanosine-5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.80 | 0.83 | 77 | empty |
| 2 | 1017 | 0.79 | 0.81 | 76 | 8GT, MG |
| 3 | 810 | 0.76 | 0.80 | 57 | empty |
| 4 | 783 | 0.73 | 0.79 | 52 | empty |
| 5 | 73 | 0.42 | 0.81 | 16 | empty |
Interfaces
9 interfaces between chains.
- A–B · 990 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–G · 942 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 653 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- G–H · 637 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- F–H · 579 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5C5J · Poymerase Nucleotide complex · the same entry in another collection · chain F against F, 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 W8STT9
- Elsewhere: RCSB PDB 5C5J · PDBe 5C5J · UniProt W8STT9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.