Research workbench
MsDpo4-DNA complex 6
Analyse MsDpo4-DNA complex 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JUS
- Type
- protein + DNA
- Length
- 737 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155); SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3')
- EC
- 2.7.7.7
- UniProt
- A0QR77
- Ligands
- 2TM, MN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.5 · 4 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DNA polymerase IV (EC 2.7.7.7) | protein | 347 | 39% helix, 24% strand | A0QR77 |
| B | DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3') | dna | 13 | — | — |
| C, H | DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3') | dna | 9 | — | — |
| G | DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- 2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · 2 copies · chains A, B, C, F, G, H
- MN · Manganese (II) 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.80 | 0.81 | 81 | 2TM |
| 2 | 945 | 0.79 | 0.81 | 73 | 2TM, MN |
| 3 | 636 | 0.73 | 0.80 | 52 | empty |
| 4 | 767 | 0.71 | 0.78 | 57 | empty |
| 5 | 73 | 0.42 | 0.80 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1015 Ų buried · 17 hydrogen bonds · protein-nucleic
- F–G · 837 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–H · 613 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 575 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–F · 434 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6JUS · MSDPO4-DNA complex 6 · 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 6JUS · PDBe 6JUS · UniProt A0QR77
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