Research workbench
MsDpo4-DNA complex 1
Analyse MsDpo4-DNA complex 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JUL
- Type
- protein + DNA
- Length
- 735 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mycobacterium smegmatis str. MC2 155; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
- EC
- 2.7.7.7
- UniProt
- A0QR77
- Ligands
- 0KX, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.3 · 5 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A | DNA polymerase IV (EC 2.7.7.7) | protein | 347 | 41% helix, 24% strand | A0QR77 |
| H | DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 8 | — | — |
| G | DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 10 | — | — |
| B | DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 12 | — | — |
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 | 1037 | 0.80 | 0.81 | 78 | 0KX, MG |
| 2 | 912 | 0.78 | 0.81 | 62 | 0KX, MG |
| 3 | 491 | 0.73 | 0.82 | 35 | empty |
| 4 | 590 | 0.71 | 0.80 | 45 | empty |
| 5 | 104 | 0.48 | 0.81 | 17 | empty |
Interfaces
9 interfaces between chains.
- F–G · 883 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 807 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 561 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–H · 559 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–A · 456 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 6JUL · MSDPO4-DNA complex 1 · 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 6JUL · PDBe 6JUL · UniProt A0QR77
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