MolNFT v1 · #65045 · protein
Crystal structure of the E. COLI clamp loader bound to psi peptide
3GLH · DNA polymerase III subunit delta: “Crystal structure of the E. COLI clamp loader bound to psi peptide”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #65045 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GLH
- Type
- protein
- Length
- 5,277 residues
- Chains
- 15
- 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
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K | DNA polymerase III subunit delta (EC 2.7.7.7) | protein | 336 | 55% helix, 11% strand | P28630 |
| B, C, G, H, L, M | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 364 | 54% helix, 8% strand | P06710 |
| D, I, N | DNA polymerase III subunit tau (EC 2.7.7.7) | protein | 363 | 52% helix, 8% strand | P06710 |
| E, J, O | DNA polymerase III subunit delta' (EC 2.7.7.7) | protein | 332 | 52% helix, 8% strand | P28631 |
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 | 1019 | 0.83 | 0.84 | 110 | empty |
| 2 | 945 | 0.82 | 0.84 | 106 | empty |
| 3 | 944 | 0.81 | 0.83 | 103 | empty |
| 4 | 870 | 0.81 | 0.83 | 81 | empty |
| 5 | 684 | 0.80 | 0.85 | 76 | empty |
Interfaces
29 interfaces between chains.
- C–D · 2754 Ų buried · 26 hydrogen bonds · protein-protein
- M–N · 2726 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 2698 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1982 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1966 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3GLH · Crystal Structure of the E. coli clamp loader bound to Psi Peptide · the same entry in another collection · chain J against J, 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 3GLH · PDBe 3GLH · UniProt P28630 · UniProt P06710 · UniProt P28631
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