MolNFT v1 · #153921 · protein + DNA
MSDPO4-DNA complex 5
6JUR · DNA polymerase IV: “MSDPO4-DNA complex 5”. X-ray diffraction, 2 ligands (2TM, MN), 5 pockets (best druggability 0.79). MolNFT v1 #153921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JUR
- Type
- protein + DNA
- Length
- 734 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*A)-3')
- EC
- 2.7.7.7
- UniProt
- A0QR77
- Ligands
- 2TM, MN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 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, G | DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*A)-3') | dna | 12 | — | — |
| C, H | DNA (5'-D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*A)-3') | dna | 8 | — | — |
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 | 931 | 0.79 | 0.81 | 74 | 2TM, MN |
| 2 | 926 | 0.78 | 0.81 | 70 | 2TM, MN |
| 3 | 748 | 0.72 | 0.78 | 51 | empty |
| 4 | 666 | 0.71 | 0.79 | 54 | empty |
| 5 | 53 | 0.32 | 0.77 | 13 | empty |
Interfaces
9 interfaces between chains.
- A–B · 979 Ų buried · 23 hydrogen bonds · protein-nucleic
- F–G · 901 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 598 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–H · 586 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–F · 493 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6JUR · MsDpo4-DNA complex 5 · 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 6JUR · PDBe 6JUR · UniProt A0QR77
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