MolNFT v1 · #138953 · protein
DNA replication regulation protein
5X06 · DNA polymerase III subunit beta: “DNA replication regulation protein”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.76). MolNFT v1 #138953 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X06
- Type
- protein
- Length
- 2,300 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; Dnaa regulatory inactivator hda
- EC
- 2.7.7.7
- UniProt
- P0A990, P69933
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 364 | 21% helix, 46% strand | P0A990 |
| E | Dnaa regulatory inactivator hda | protein | 220 | 50% helix, 11% strand | P69933 |
| F | Dnaa regulatory inactivator hda | protein | 228 | 49% helix, 11% strand | P69933 |
| G | Dnaa regulatory inactivator hda | protein | 205 | 47% helix, 11% strand | P69933 |
| H | Dnaa regulatory inactivator hda | protein | 191 | 47% helix, 13% strand | P69933 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains E, F, G, H
- GOL · Glycerol · additive · 4 copies · chains C, D, H, A, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.76 | 0.79 | 71 | ADP, MG |
| 2 | 952 | 0.75 | 0.78 | 66 | ADP, MG |
| 3 | 921 | 0.75 | 0.78 | 70 | ADP, MG |
| 4 | 451 | 0.69 | 0.80 | 49 | ADP, MG |
| 5 | 432 | 0.67 | 0.79 | 32 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1419 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 1403 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1360 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1321 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 1206 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 P0A990
- Every structure of UniProt P69933
- Elsewhere: RCSB PDB 5X06 · PDBe 5X06 · UniProt P0A990 · UniProt P69933
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