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Crystal structure of the E. COLI clamp loader bound to psi peptide

Analyse Crystal structure of the E. COLI clamp loader bound to psi peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 26 hydrogen bonds · protein-protein
M–N · 2726 Å² buried · 27 hydrogen bonds · protein-protein
H–I · 2698 Å² buried · 20 hydrogen bonds · protein-protein
I–J · 1982 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1966 Å² 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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