Research workbench
MsDpo4-DNA complex 4
Analyse MsDpo4-DNA complex 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JUO
- Type
- protein + DNA
- Length
- 738 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.16
- Source
- Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155); SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3')
- EC
- 2.7.7.7
- UniProt
- A0QR77
- Ligands
- 0KX, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.16 · 5 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DNA polymerase IV (EC 2.7.7.7) | protein | 347 | 40% helix, 24% strand | A0QR77 |
| B | DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3') | dna | 13 | — | — |
| C | DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3') | dna | 12 | — | — |
| G | DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3') | dna | 11 | — | — |
| H | DNA (5'-D(P*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains A, B, C, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains A, C, F, H
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 | 940 | 0.79 | 0.81 | 65 | 0KX, MG |
| 2 | 880 | 0.78 | 0.81 | 66 | 0KX, MG |
| 3 | 875 | 0.73 | 0.78 | 52 | empty |
| 4 | 781 | 0.72 | 0.78 | 53 | empty |
| 5 | 94 | 0.47 | 0.81 | 14 | empty |
Interfaces
9 interfaces between chains.
- F–G · 860 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 810 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–H · 564 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 554 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 464 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 6JUO · MSDPO4-DNA complex 4 · 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 A0QR77
- Elsewhere: RCSB PDB 6JUO · PDBe 6JUO · UniProt A0QR77
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