MolNFT v1 · #153917 · protein + DNA
MSDPO4-DNA complex 3
6JUN · DNA polymerase IV: “MSDPO4-DNA complex 3”. X-ray diffraction, 2 ligands (0KX, MG), 7 pockets (best druggability 0.79). MolNFT v1 #153917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JUN
- Type
- protein + DNA
- Length
- 732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')
- EC
- 2.7.7.7
- UniProt
- A0QR77
- Ligands
- 0KX, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 347 | 42% helix, 23% strand | A0QR77 |
| H, C | DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 8 | — | — |
| G, B | DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains F, H, G, A, C, B
- MG · Magnesium ion · metal · 4 copies · chains F, H, A, C
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 | 985 | 0.79 | 0.81 | 84 | 0KX, MG |
| 2 | 932 | 0.78 | 0.81 | 74 | MG, 0KX |
| 3 | 757 | 0.73 | 0.79 | 51 | empty |
| 4 | 737 | 0.72 | 0.78 | 51 | empty |
| 5 | 68 | 0.49 | 0.85 | 14 | empty |
Interfaces
9 interfaces between chains.
- A–B · 847 Ų buried · 17 hydrogen bonds · protein-nucleic
- F–G · 841 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–H · 604 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 577 Ų buried · 16 hydrogen bonds · protein-nucleic
- F–A · 449 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JUN · MsDpo4-DNA complex 3 · 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 A0QR77
- Elsewhere: RCSB PDB 6JUN · PDBe 6JUN · UniProt A0QR77
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