MolNFT v1 · #65043 · protein + DNA
Crystal structure of the ecoli clamp loader bound to primer-template DNA
3GLF · DNA polymerase III subunit delta: “Crystal structure of the ecoli clamp loader bound to primer-template DNA”. X-ray diffraction, 4 ligands (ADP, BEF, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #65043 on GenesisL1: 3D…
- PDB
- 3GLF
- Type
- protein + DNA
- Length
- 3,578 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit delta; DNA polymerase III subunit tau; DNA polymerase III…
- EC
- 2.7.7.7
- UniProt
- P28630, P06710, P28631
- Ligands
- ADP, BEF, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DNA polymerase III subunit delta (EC 2.7.7.7) | protein | 333 | 51% helix, 11% strand | P28630 |
| B | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 364 | 56% helix, 8% strand | P06710 |
| C, H | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 365 | 55% helix, 8% strand | P06710 |
| D, I | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 362 | 57% helix, 8% strand | P06710 |
| E, J | DNA polymerase III subunit delta' (EC 2.7.7.7) | protein | 334 | 54% helix, 9% strand | P28631 |
| G | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 378 | 54% helix, 7% strand | P06710 |
| K, M | DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)- 3') | dna | 14 | — | — |
| L, N | DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains B, C, D, E, G, H, I, J
- BEF · Beryllium trifluoride ion · ligand · 6 copies · chains B, C, D, E, G, H, I, J
- ZN · Zinc ion · metal · 8 copies · chains B, C, D, E, G, H, I, J
- MG · Magnesium ion · metal · 6 copies · chains B, C, D, E, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.83 | 0.85 | 83 | empty |
| 2 | 1121 | 0.82 | 0.83 | 104 | empty |
| 3 | 825 | 0.80 | 0.83 | 62 | empty |
| 4 | 924 | 0.79 | 0.82 | 112 | empty |
| 5 | 703 | 0.79 | 0.83 | 79 | empty |
Interfaces
39 interfaces between chains.
- G–H · 2974 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2738 Ų buried · 30 hydrogen bonds · protein-protein
- H–I · 2516 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2430 Ų buried · 30 hydrogen bonds · protein-protein
- I–J · 2394 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3GLF · Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA · the same entry in another collection · chain N against N, 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 P28630
- Every structure of UniProt P06710
- Every structure of UniProt P28631
- Elsewhere: RCSB PDB 3GLF · PDBe 3GLF · UniProt P28630 · UniProt P06710 · UniProt P28631
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