Research workbench
MSDPO4-DNA complex 2
Analyse MSDPO4-DNA complex 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JUM
- Type
- protein + DNA
- Length
- 737 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
- 9 · best druggability 0.75
Structure
x-ray diffraction · 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 |
| H | DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 8 | — | — |
| G | DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 12 | — | — |
| C | DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 10 | — | — |
| B | DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains A, C, B, F, H, G
- 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.75 | 0.82 | 43 | empty |
| 2 | 684 | 0.74 | 0.81 | 52 | empty |
| 3 | 666 | 0.74 | 0.80 | 43 | empty |
| 4 | 817 | 0.72 | 0.77 | 55 | empty |
| 5 | 288 | 0.62 | 0.80 | 38 | 0KX, MG |
Interfaces
9 interfaces between chains.
- F–G · 847 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 806 Ų buried · 16 hydrogen bonds · protein-nucleic
- F–H · 596 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 584 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–B · 465 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 6JUM · MsDpo4-DNA complex 2 · 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 6JUM · PDBe 6JUM · UniProt A0QR77
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