Research workbench
Crystal structure of the E. COLI clamp loader bound to primer-template DNA and psi peptide
Analyse Crystal structure of the E. COLI clamp loader bound to primer-template DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GLI
- Type
- protein + DNA
- Length
- 3,623 residues
- Chains
- 16
- 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, P28632
- Ligands
- ADP, BEF, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit delta (EC 2.7.7.7) | protein | 333 | 55% helix, 11% strand | P28630 |
| B | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 359 | 56% helix, 9% strand | P06710 |
| C, H | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 365 | 56% helix, 8% strand | P06710 |
| D, I | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 362 | 59% helix, 7% strand | P06710 |
| E, J | DNA polymerase III subunit delta' (EC 2.7.7.7) | protein | 334 | 55% helix, 9% strand | P28631 |
| F | DNA polymerase III subunit delta (EC 2.7.7.7) | protein | 334 | 55% helix, 11% strand | P28630 |
| G | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 373 | 55% helix, 9% 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 | — | — |
| O, P | DNA polymerase III subunit psi (EC 2.7.7.7) | protein | 27 | 44% helix, 15% strand | P28632 |
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 | 1102 | 0.87 | 0.88 | 114 | empty |
| 2 | 1031 | 0.83 | 0.84 | 102 | empty |
| 3 | 866 | 0.82 | 0.85 | 91 | empty |
| 4 | 134 | 0.81 | 0.97 | 30 | empty |
| 5 | 119 | 0.80 | 0.97 | 27 | empty |
Interfaces
48 interfaces between chains.
- G–H · 2841 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2604 Ų buried · 35 hydrogen bonds · protein-protein
- H–I · 2475 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2422 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 2374 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3GLI · Crystal Structure of the E. coli clamp loader bound to Primer-Template DNA and Psi Peptide · the same entry in another collection · chain G against G, 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
- Every structure of UniProt P28632
- Elsewhere: RCSB PDB 3GLI · PDBe 3GLI · UniProt P28630 · UniProt P06710 · UniProt P28631 · UniProt P28632
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